| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:15:28 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the seqbias package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/seqbias.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1827/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| seqbias 1.47.0 (landing page) Daniel Jones
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: seqbias |
| Version: 1.47.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:seqbias.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings seqbias_1.47.0.tar.gz |
| StartedAt: 2023-02-07 15:22:06 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 15:25:10 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 184.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: seqbias.Rcheck |
| Warnings: 2 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:seqbias.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings seqbias_1.47.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/seqbias.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘seqbias/DESCRIPTION’ ... OK
* this is package ‘seqbias’ version ‘1.47.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘seqbias’ can be installed ... WARNING
Found the following significant warnings:
./yaml-cpp/parser.h:45:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
./yaml-cpp/parser.h:46:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
./yaml-cpp/iterator.h:20:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
./yaml-cpp/iterator.h:36:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
./yaml-cpp/node.h:43:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
./yaml-cpp/node.h:115:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
./yaml-cpp/emitter.h:98:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
sequencing_bias.cpp:398:9: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
sequencing_bias.cpp:628:9: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
yaml-cpp/ptr_stack.h:29:24: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
yaml-cpp/ptr_stack.h:33:14: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
yaml-cpp/ptr_stack.h:34:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
yaml-cpp/setting.h:24:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
yaml-cpp/setting.h:59:21: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
yaml-cpp/setting.h:60:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
yaml-cpp/setting.h:84:32: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
yaml-cpp/emitterstate.cpp:51:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
yaml-cpp/emitterstate.cpp:71:30: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
yaml-cpp/iterator.cpp:11:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
yaml-cpp/ptr_vector.h:31:37: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
yaml-cpp/node.cpp:54:14: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
yaml-cpp/node.cpp:56:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
yaml-cpp/node.cpp:148:54: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
yaml-cpp/node.cpp:150:54: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
yaml-cpp/node.cpp:166:54: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
yaml-cpp/node.cpp:168:54: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
yaml-cpp/nodeownership.cpp:18:40: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
yaml-cpp/singledocparser.h:56:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
yaml-cpp/scanner.cpp:237:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
yaml-cpp/scanner.cpp:284:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
See ‘/home/biocbuild/bbs-3.17-bioc/meat/seqbias.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
installed size is 10.0Mb
sub-directories of 1Mb or more:
libs 9.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘GenomicRanges’ which was already attached by Depends.
Please remove these calls from your code.
Packages in Depends field not imported from:
‘Biostrings’ ‘GenomicRanges’ ‘methods’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
count.reads: no visible global function definition for ‘is’
count.reads : <anonymous>: no visible global function definition for
‘seqnames’
count.reads : <anonymous>: no visible global function definition for
‘start’
count.reads : <anonymous>: no visible global function definition for
‘end’
count.reads : <anonymous>: no visible global function definition for
‘strand’
random.intervals: no visible global function definition for ‘is’
random.intervals : uniform_ints : <anonymous>: no visible global
function definition for ‘runif’
random.intervals: no visible global function definition for ‘GRanges’
random.intervals: no visible global function definition for ‘IRanges’
seqbias.fit: no visible global function definition for ‘new’
seqbias.load: no visible global function definition for ‘new’
seqbias.predict: no visible global function definition for ‘is’
seqbias.predict : <anonymous>: no visible global function definition
for ‘seqnames’
seqbias.predict : <anonymous>: no visible global function definition
for ‘start’
seqbias.predict : <anonymous>: no visible global function definition
for ‘end’
seqbias.predict : <anonymous>: no visible global function definition
for ‘strand’
Undefined global functions or variables:
GRanges IRanges end is new runif seqnames start strand
Consider adding
importFrom("methods", "is", "new")
importFrom("stats", "end", "runif", "start")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.17-bioc/R/library/seqbias/libs/seqbias.so’:
Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
Found ‘abort’, possibly from ‘abort’ (C)
Found ‘exit’, possibly from ‘exit’ (C)
Found ‘rand’, possibly from ‘rand’ (C)
Found ‘stderr’, possibly from ‘stderr’ (C)
Found ‘stdout’, possibly from ‘stdout’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
seqbias_save 3.275 2.009 23.46
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘overview.Rnw’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 4 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/seqbias.Rcheck/00check.log’
for details.
seqbias.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL seqbias
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘seqbias’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
$SEQBIAS_OBJ is [common.o miscmath.o pos_table.o kmer_matrix.o logger.o motif.o seqbias.o sequencing_bias.o twobitseq.o]
$YAML_CPP_OBJ is [aliasmanager.o conversion.o directives.o emitfromevents.o emitter.o emitterstate.o emitterutils.o exp.o iterator.o nodebuilder.o node.o nodeownership.o null.o ostream.o parser.o regex.o scanner.o scanscalar.o scantag.o scantoken.o simplekey.o singledocparser.o stream.o tag.o]
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c common.c -o common.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c miscmath.c -o miscmath.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c pos_table.c -o pos_table.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c kmer_matrix.cpp -o kmer_matrix.o
In file included from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
./yaml-cpp/parser.h:45:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
45 | std::auto_ptr<Scanner> m_pScanner;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
./yaml-cpp/parser.h:46:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
46 | std::auto_ptr<Directives> m_pDirectives;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
./yaml-cpp/iterator.h:20:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
20 | Iterator(std::auto_ptr<IterPriv> pData);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
./yaml-cpp/iterator.h:36:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
36 | std::auto_ptr<IterPriv> m_pData;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
./yaml-cpp/node.h:43:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
43 | std::auto_ptr<Node> Clone() const;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
./yaml-cpp/node.h:115:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
115 | std::auto_ptr<NodeOwnership> m_pOwnership;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:13,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
./yaml-cpp/emitter.h:98:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
98 | std::auto_ptr <EmitterState> m_pState;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c logger.cpp -o logger.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c motif.cpp -o motif.o
In file included from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
./yaml-cpp/parser.h:45:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
45 | std::auto_ptr<Scanner> m_pScanner;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
./yaml-cpp/parser.h:46:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
46 | std::auto_ptr<Directives> m_pDirectives;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
./yaml-cpp/iterator.h:20:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
20 | Iterator(std::auto_ptr<IterPriv> pData);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
./yaml-cpp/iterator.h:36:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
36 | std::auto_ptr<IterPriv> m_pData;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
./yaml-cpp/node.h:43:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
43 | std::auto_ptr<Node> Clone() const;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
./yaml-cpp/node.h:115:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
115 | std::auto_ptr<NodeOwnership> m_pOwnership;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:13,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
./yaml-cpp/emitter.h:98:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
98 | std::auto_ptr <EmitterState> m_pState;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from motif.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c seqbias.cpp -o seqbias.o
In file included from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
./yaml-cpp/parser.h:45:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
45 | std::auto_ptr<Scanner> m_pScanner;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
./yaml-cpp/parser.h:46:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
46 | std::auto_ptr<Directives> m_pDirectives;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
./yaml-cpp/iterator.h:20:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
20 | Iterator(std::auto_ptr<IterPriv> pData);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
./yaml-cpp/iterator.h:36:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
36 | std::auto_ptr<IterPriv> m_pData;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
./yaml-cpp/node.h:43:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
43 | std::auto_ptr<Node> Clone() const;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
./yaml-cpp/node.h:115:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
115 | std::auto_ptr<NodeOwnership> m_pOwnership;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:13,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
./yaml-cpp/emitter.h:98:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
98 | std::auto_ptr <EmitterState> m_pState;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from seqbias.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
seqbias.cpp: In function ‘void R_init_seqbias(DllInfo*)’:
seqbias.cpp:493:34: warning: cast between incompatible function types from ‘SEXPREC* (*)(SEXP, SEXP, SEXP, SEXP, SEXP)’ {aka ‘SEXPREC* (*)(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’} to ‘DL_FUNC’ {aka ‘void* (*)()’} [-Wcast-function-type]
493 | { "seqbias_fit", (DL_FUNC) &seqbias_fit, 5 },
| ^~~~~~~~~~~~~~~~~~~~~~
seqbias.cpp:494:34: warning: cast between incompatible function types from ‘SEXPREC* (*)(SEXP, SEXP, SEXP, SEXP, SEXP)’ {aka ‘SEXPREC* (*)(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’} to ‘DL_FUNC’ {aka ‘void* (*)()’} [-Wcast-function-type]
494 | { "seqbias_predict", (DL_FUNC) &seqbias_predict, 5 },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
seqbias.cpp:495:34: warning: cast between incompatible function types from ‘SEXPREC* (*)(SEXP, SEXP)’ {aka ‘SEXPREC* (*)(SEXPREC*, SEXPREC*)’} to ‘DL_FUNC’ {aka ‘void* (*)()’} [-Wcast-function-type]
495 | { "seqbias_load", (DL_FUNC) &seqbias_load, 2 },
| ^~~~~~~~~~~~~~~~~~~~~~~
seqbias.cpp:496:34: warning: cast between incompatible function types from ‘SEXPREC* (*)(SEXP, SEXP)’ {aka ‘SEXPREC* (*)(SEXPREC*, SEXPREC*)’} to ‘DL_FUNC’ {aka ‘void* (*)()’} [-Wcast-function-type]
496 | { "seqbias_save", (DL_FUNC) &seqbias_save, 2 },
| ^~~~~~~~~~~~~~~~~~~~~~~
seqbias.cpp:497:37: warning: cast between incompatible function types from ‘SEXPREC* (*)(SEXP)’ {aka ‘SEXPREC* (*)(SEXPREC*)’} to ‘DL_FUNC’ {aka ‘void* (*)()’} [-Wcast-function-type]
497 | { "seqbias_open_bam", (DL_FUNC) &seqbias_open_bam, 1 },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
seqbias.cpp:498:37: warning: cast between incompatible function types from ‘SEXPREC* (*)(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’ {aka ‘SEXPREC* (*)(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’} to ‘DL_FUNC’ {aka ‘void* (*)()’} [-Wcast-function-type]
498 | { "seqbias_count_reads", (DL_FUNC) &seqbias_count_reads, 7 },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
seqbias.cpp:499:49: warning: cast between incompatible function types from ‘SEXPREC* (*)(SEXP, SEXP)’ {aka ‘SEXPREC* (*)(SEXPREC*, SEXPREC*)’} to ‘DL_FUNC’ {aka ‘void* (*)()’} [-Wcast-function-type]
499 | { "seqbias_alloc_kmer_matrix", (DL_FUNC) &seqbias_alloc_kmer_matrix, 2 },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
seqbias.cpp:500:49: warning: cast between incompatible function types from ‘SEXPREC* (*)(SEXP, SEXP, SEXP, SEXP)’ {aka ‘SEXPREC* (*)(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’} to ‘DL_FUNC’ {aka ‘void* (*)()’} [-Wcast-function-type]
500 | { "seqbias_tally_kmers", (DL_FUNC) &seqbias_tally_kmers, 4 },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
seqbias.cpp:501:49: warning: cast between incompatible function types from ‘SEXPREC* (*)(SEXP, SEXP)’ {aka ‘SEXPREC* (*)(SEXPREC*, SEXPREC*)’} to ‘DL_FUNC’ {aka ‘void* (*)()’} [-Wcast-function-type]
501 | { "sebqias_dataframe_from_kmer_matrix", (DL_FUNC) &seqbias_dataframe_from_kmer_matrix, 2 },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c sequencing_bias.cpp -o sequencing_bias.o
In file included from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
./yaml-cpp/parser.h:45:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
45 | std::auto_ptr<Scanner> m_pScanner;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
./yaml-cpp/parser.h:46:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
46 | std::auto_ptr<Directives> m_pDirectives;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
./yaml-cpp/iterator.h:20:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
20 | Iterator(std::auto_ptr<IterPriv> pData);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
./yaml-cpp/iterator.h:36:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
36 | std::auto_ptr<IterPriv> m_pData;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
./yaml-cpp/node.h:43:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
43 | std::auto_ptr<Node> Clone() const;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:10,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
./yaml-cpp/node.h:115:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
115 | std::auto_ptr<NodeOwnership> m_pOwnership;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/yaml.h:13,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
./yaml-cpp/emitter.h:98:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
98 | std::auto_ptr <EmitterState> m_pState;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from motif.hpp:13,
from sequencing_bias.hpp:13,
from sequencing_bias.cpp:8:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
sequencing_bias.cpp: In member function ‘void sequencing_bias::build(const char*, pos_table*, size_t, pos_t, pos_t, double)’:
sequencing_bias.cpp:398:9: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
398 | free(local_seq);
| ~~~~^~~~~~~~~~~
sequencing_bias.cpp:301:37: note: returned from ‘void* operator new [](std::size_t)’
301 | local_seq = new char[ L + R + 2 ];
| ^
sequencing_bias.cpp: In function ‘kmer_matrix tabulate_bias(double*, pos_t, pos_t, int, const char*, const char*, const char*)’:
sequencing_bias.cpp:628:9: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
628 | free(local_seq);
| ~~~~^~~~~~~~~~~
sequencing_bias.cpp:541:51: note: returned from ‘void* operator new [](std::size_t)’
541 | local_seq = new char[ (k - 1) + L + 1 + R + 1 ];
| ^
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c twobitseq.cpp -o twobitseq.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c yaml-cpp/aliasmanager.cpp -o yaml-cpp/aliasmanager.o
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/aliasmanager.cpp:2:
./yaml-cpp/iterator.h:20:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
20 | Iterator(std::auto_ptr<IterPriv> pData);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/aliasmanager.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/aliasmanager.cpp:2:
./yaml-cpp/iterator.h:36:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
36 | std::auto_ptr<IterPriv> m_pData;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/aliasmanager.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/aliasmanager.cpp:2:
./yaml-cpp/node.h:43:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
43 | std::auto_ptr<Node> Clone() const;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/aliasmanager.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/aliasmanager.cpp:2:
./yaml-cpp/node.h:115:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
115 | std::auto_ptr<NodeOwnership> m_pOwnership;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/aliasmanager.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c yaml-cpp/directives.cpp -o yaml-cpp/directives.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c yaml-cpp/emitfromevents.cpp -o yaml-cpp/emitfromevents.o
In file included from yaml-cpp/emitfromevents.cpp:2:
./yaml-cpp/emitter.h:98:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
98 | std::auto_ptr <EmitterState> m_pState;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitfromevents.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
In file included from yaml-cpp/emitter.cpp:1:
./yaml-cpp/emitter.h:98:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
98 | std::auto_ptr <EmitterState> m_pState;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitter.cpp:2:
yaml-cpp/ptr_stack.h:29:24: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
29 | void push(std::auto_ptr<T> t) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitter.cpp:2:
yaml-cpp/ptr_stack.h:33:14: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
33 | std::auto_ptr<T> pop() {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitter.cpp:2:
yaml-cpp/ptr_stack.h: In member function ‘std::auto_ptr<_Up> ptr_stack<T>::pop()’:
yaml-cpp/ptr_stack.h:34:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
34 | std::auto_ptr<T> t(m_data.back());
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:10,
from yaml-cpp/emitter.cpp:2:
yaml-cpp/setting.h: At global scope:
yaml-cpp/setting.h:24:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
24 | std::auto_ptr <SettingChangeBase> set(const T& value);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:10,
from yaml-cpp/emitter.cpp:2:
yaml-cpp/setting.h:59:21: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
59 | inline std::auto_ptr <SettingChangeBase> Setting<T>::set(const T& value) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:10,
from yaml-cpp/emitter.cpp:2:
yaml-cpp/setting.h: In member function ‘std::auto_ptr<YAML::SettingChangeBase> YAML::Setting<T>::set(const T&)’:
yaml-cpp/setting.h:60:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
60 | std::auto_ptr <SettingChangeBase> pChange(new SettingChange<T> (this));
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:10,
from yaml-cpp/emitter.cpp:2:
yaml-cpp/setting.h: At global scope:
yaml-cpp/setting.h:84:32: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
84 | void push(std::auto_ptr <SettingChangeBase> pSettingChange) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
In file included from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/ptr_stack.h:29:24: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
29 | void push(std::auto_ptr<T> t) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/ptr_stack.h:33:14: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
33 | std::auto_ptr<T> pop() {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/ptr_stack.h: In member function ‘std::auto_ptr<T> ptr_stack<T>::pop()’:
yaml-cpp/ptr_stack.h:34:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
34 | std::auto_ptr<T> t(m_data.back());
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:10,
from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/setting.h: At global scope:
yaml-cpp/setting.h:24:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
24 | std::auto_ptr <SettingChangeBase> set(const T& value);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:10,
from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/setting.h:59:21: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
59 | inline std::auto_ptr <SettingChangeBase> Setting<T>::set(const T& value) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:10,
from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/setting.h: In member function ‘std::auto_ptr<YAML::SettingChangeBase> YAML::Setting<T>::set(const T&)’:
yaml-cpp/setting.h:60:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
60 | std::auto_ptr <SettingChangeBase> pChange(new SettingChange<T> (this));
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:10,
from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/setting.h: At global scope:
yaml-cpp/setting.h:84:32: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
84 | void push(std::auto_ptr <SettingChangeBase> pSettingChange) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
yaml-cpp/emitterstate.cpp: In member function ‘void YAML::EmitterState::BeginGroup(YAML::GROUP_TYPE)’:
yaml-cpp/emitterstate.cpp:51:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
51 | std::auto_ptr<Group> pGroup(new Group(type));
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
yaml-cpp/emitterstate.cpp: In member function ‘void YAML::EmitterState::EndGroup(YAML::GROUP_TYPE)’:
yaml-cpp/emitterstate.cpp:71:30: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
71 | std::auto_ptr<Group> pFinishedGroup = m_groups.pop();
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/iterator.cpp:1:
./yaml-cpp/iterator.h:20:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
20 | Iterator(std::auto_ptr<IterPriv> pData);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/iterator.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/iterator.cpp:1:
./yaml-cpp/iterator.h:36:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
36 | std::auto_ptr<IterPriv> m_pData;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/iterator.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/iterator.cpp:1:
./yaml-cpp/node.h:43:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
43 | std::auto_ptr<Node> Clone() const;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/iterator.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/iterator.cpp:1:
./yaml-cpp/node.h:115:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
115 | std::auto_ptr<NodeOwnership> m_pOwnership;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/iterator.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
yaml-cpp/iterator.cpp:11:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
11 | Iterator::Iterator(std::auto_ptr<IterPriv> pData): m_pData(pData)
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/iterator.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c yaml-cpp/nodebuilder.cpp -o yaml-cpp/nodebuilder.o
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/nodebuilder.cpp:3:
./yaml-cpp/iterator.h:20:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
20 | Iterator(std::auto_ptr<IterPriv> pData);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/nodebuilder.h:10,
from yaml-cpp/nodebuilder.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/nodebuilder.cpp:3:
./yaml-cpp/iterator.h:36:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
36 | std::auto_ptr<IterPriv> m_pData;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/nodebuilder.h:10,
from yaml-cpp/nodebuilder.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/nodebuilder.cpp:3:
./yaml-cpp/node.h:43:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
43 | std::auto_ptr<Node> Clone() const;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/nodebuilder.h:10,
from yaml-cpp/nodebuilder.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/nodebuilder.cpp:3:
./yaml-cpp/node.h:115:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
115 | std::auto_ptr<NodeOwnership> m_pOwnership;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/nodebuilder.h:10,
from yaml-cpp/nodebuilder.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c yaml-cpp/node.cpp -o yaml-cpp/node.o
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
./yaml-cpp/iterator.h:20:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
20 | Iterator(std::auto_ptr<IterPriv> pData);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
./yaml-cpp/iterator.h:36:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
36 | std::auto_ptr<IterPriv> m_pData;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/node.cpp:1:
./yaml-cpp/node.h:43:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
43 | std::auto_ptr<Node> Clone() const;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/node.cpp:1:
./yaml-cpp/node.h:115:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
115 | std::auto_ptr<NodeOwnership> m_pOwnership;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/nodeownership.h:10,
from yaml-cpp/node.cpp:4:
yaml-cpp/ptr_vector.h:31:37: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
31 | void push_back(std::auto_ptr<T> t) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/node.cpp:10:
./yaml-cpp/emitter.h:98:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
98 | std::auto_ptr <EmitterState> m_pState;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
yaml-cpp/node.cpp:54:14: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
54 | std::auto_ptr<Node> Node::Clone() const
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
yaml-cpp/node.cpp: In member function ‘std::auto_ptr<YAML::Node> YAML::Node::Clone() const’:
yaml-cpp/node.cpp:56:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
56 | std::auto_ptr<Node> pNode(new Node);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
yaml-cpp/node.cpp: In member function ‘YAML::Iterator YAML::Node::begin() const’:
yaml-cpp/node.cpp:148:54: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
148 | return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_seqData.begin())));
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
yaml-cpp/node.cpp:150:54: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
150 | return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_mapData.begin())));
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
yaml-cpp/node.cpp: In member function ‘YAML::Iterator YAML::Node::end() const’:
yaml-cpp/node.cpp:166:54: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
166 | return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_seqData.end())));
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
yaml-cpp/node.cpp:168:54: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
168 | return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_mapData.end())));
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c yaml-cpp/nodeownership.cpp -o yaml-cpp/nodeownership.o
In file included from yaml-cpp/nodeownership.h:10,
from yaml-cpp/nodeownership.cpp:1:
yaml-cpp/ptr_vector.h:31:37: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
31 | void push_back(std::auto_ptr<T> t) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/nodeownership.h:10,
from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/nodeownership.cpp:2:
./yaml-cpp/iterator.h:20:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
20 | Iterator(std::auto_ptr<IterPriv> pData);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/nodeownership.h:10,
from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/nodeownership.cpp:2:
./yaml-cpp/iterator.h:36:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
36 | std::auto_ptr<IterPriv> m_pData;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/nodeownership.h:10,
from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/nodeownership.cpp:2:
./yaml-cpp/node.h:43:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
43 | std::auto_ptr<Node> Clone() const;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/nodeownership.h:10,
from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/nodeownership.cpp:2:
./yaml-cpp/node.h:115:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
115 | std::auto_ptr<NodeOwnership> m_pOwnership;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/nodeownership.h:10,
from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
yaml-cpp/nodeownership.cpp: In member function ‘YAML::Node& YAML::NodeOwnership::_Create()’:
yaml-cpp/nodeownership.cpp:18:40: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
18 | m_nodes.push_back(std::auto_ptr<Node>(new Node));
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/nodeownership.h:10,
from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c yaml-cpp/null.cpp -o yaml-cpp/null.o
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/null.cpp:2:
./yaml-cpp/iterator.h:20:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
20 | Iterator(std::auto_ptr<IterPriv> pData);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/null.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/null.cpp:2:
./yaml-cpp/iterator.h:36:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
36 | std::auto_ptr<IterPriv> m_pData;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/null.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/null.cpp:2:
./yaml-cpp/node.h:43:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
43 | std::auto_ptr<Node> Clone() const;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/null.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/null.cpp:2:
./yaml-cpp/node.h:115:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
115 | std::auto_ptr<NodeOwnership> m_pOwnership;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/null.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
In file included from yaml-cpp/parser.cpp:1:
./yaml-cpp/parser.h:45:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
45 | std::auto_ptr<Scanner> m_pScanner;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/parser.cpp:1:
./yaml-cpp/parser.h:46:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
46 | std::auto_ptr<Directives> m_pDirectives;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/parser.cpp:5:
./yaml-cpp/iterator.h:20:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
20 | Iterator(std::auto_ptr<IterPriv> pData);
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/parser.cpp:5:
./yaml-cpp/iterator.h:36:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
36 | std::auto_ptr<IterPriv> m_pData;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/parser.cpp:5:
./yaml-cpp/node.h:43:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
43 | std::auto_ptr<Node> Clone() const;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/parser.cpp:5:
./yaml-cpp/node.h:115:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
115 | std::auto_ptr<NodeOwnership> m_pOwnership;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/scanner.h:15,
from yaml-cpp/parser.cpp:7:
yaml-cpp/ptr_vector.h:31:37: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
31 | void push_back(std::auto_ptr<T> t) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/parser.cpp:8:
yaml-cpp/singledocparser.h:56:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
56 | std::auto_ptr<CollectionStack> m_pCollectionStack;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o
In file included from yaml-cpp/scanner.h:15,
from yaml-cpp/scanner.cpp:1:
yaml-cpp/ptr_vector.h:31:37: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
31 | void push_back(std::auto_ptr<T> t) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/scanner.h:15,
from yaml-cpp/scanner.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
yaml-cpp/scanner.cpp: In member function ‘void YAML::Scanner::StartStream()’:
yaml-cpp/scanner.cpp:237:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
237 | std::auto_ptr<IndentMarker> pIndent(new IndentMarker(-1, IndentMarker::NONE));
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/scanner.h:15,
from yaml-cpp/scanner.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
yaml-cpp/scanner.cpp: In member function ‘YAML::Scanner::IndentMarker* YAML::Scanner::PushIndentTo(int, YAML::Scanner::IndentMarker::INDENT_TYPE)’:
yaml-cpp/scanner.cpp:284:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
284 | std::auto_ptr<IndentMarker> pIndent(new IndentMarker(column, type));
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/scanner.h:15,
from yaml-cpp/scanner.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o
In file included from yaml-cpp/scanner.h:15,
from yaml-cpp/scanscalar.cpp:2:
yaml-cpp/ptr_vector.h:31:37: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
31 | void push_back(std::auto_ptr<T> t) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/scanner.h:15,
from yaml-cpp/scanscalar.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o
In file included from yaml-cpp/scanner.h:15,
from yaml-cpp/scantag.cpp:1:
yaml-cpp/ptr_vector.h:31:37: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
31 | void push_back(std::auto_ptr<T> t) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/scanner.h:15,
from yaml-cpp/scantag.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o
In file included from yaml-cpp/scanner.h:15,
from yaml-cpp/scantoken.cpp:1:
yaml-cpp/ptr_vector.h:31:37: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
31 | void push_back(std::auto_ptr<T> t) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/scanner.h:15,
from yaml-cpp/scantoken.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o
In file included from yaml-cpp/scanner.h:15,
from yaml-cpp/simplekey.cpp:1:
yaml-cpp/ptr_vector.h:31:37: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
31 | void push_back(std::auto_ptr<T> t) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/scanner.h:15,
from yaml-cpp/simplekey.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c yaml-cpp/singledocparser.cpp -o yaml-cpp/singledocparser.o
In file included from yaml-cpp/singledocparser.cpp:1:
yaml-cpp/singledocparser.h:56:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
56 | std::auto_ptr<CollectionStack> m_pCollectionStack;
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/singledocparser.h:13,
from yaml-cpp/singledocparser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from yaml-cpp/singledocparser.cpp:2:
yaml-cpp/collectionstack.h: In member function ‘void YAML::CollectionStack::PopCollectionType(YAML::CollectionType::value)’:
yaml-cpp/collectionstack.h:28:62: warning: unused parameter ‘type’ [-Wunused-parameter]
28 | void PopCollectionType(CollectionType::value type) { assert(type == GetCurCollectionType()); collectionStack.pop(); }
| ~~~~~~~~~~~~~~~~~~~~~~^~~~
In file included from yaml-cpp/scanner.h:15,
from yaml-cpp/singledocparser.cpp:6:
yaml-cpp/ptr_vector.h: At global scope:
yaml-cpp/ptr_vector.h:31:37: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
31 | void push_back(std::auto_ptr<T> t) {
| ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
from yaml-cpp/singledocparser.h:13,
from yaml-cpp/singledocparser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -g -O2 -Wall -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o seqbias.so common.o miscmath.o pos_table.o kmer_matrix.o logger.o motif.o seqbias.o sequencing_bias.o twobitseq.o yaml-cpp/aliasmanager.o yaml-cpp/conversion.o yaml-cpp/directives.o yaml-cpp/emitfromevents.o yaml-cpp/emitter.o yaml-cpp/emitterstate.o yaml-cpp/emitterutils.o yaml-cpp/exp.o yaml-cpp/iterator.o yaml-cpp/nodebuilder.o yaml-cpp/node.o yaml-cpp/nodeownership.o yaml-cpp/null.o yaml-cpp/ostream.o yaml-cpp/parser.o yaml-cpp/regex.o yaml-cpp/scanner.o yaml-cpp/scanscalar.o yaml-cpp/scantag.o yaml-cpp/scantoken.o yaml-cpp/simplekey.o yaml-cpp/singledocparser.o yaml-cpp/stream.o yaml-cpp/tag.o /home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-seqbias/00new/seqbias/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (seqbias)
seqbias.Rcheck/seqbias-Ex.timings
| name | user | system | elapsed | |
| count_reads | 0.087 | 0.004 | 0.190 | |
| kmer_freq | 0.538 | 0.009 | 0.613 | |
| random_intervals | 0.045 | 0.000 | 0.045 | |
| seqbias_fit | 2.995 | 0.031 | 3.414 | |
| seqbias_load | 2.049 | 0.016 | 2.232 | |
| seqbias_predict | 2.025 | 0.012 | 2.118 | |
| seqbias_save | 3.275 | 2.009 | 23.460 | |