| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-05-10 10:04:41 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| 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 snpStats package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/snpStats.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1925/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| snpStats 1.51.0 (landing page) David Clayton
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: snpStats |
| Version: 1.51.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:snpStats.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings snpStats_1.51.0.tar.gz |
| StartedAt: 2023-05-10 05:19:08 -0000 (Wed, 10 May 2023) |
| EndedAt: 2023-05-10 05:22:37 -0000 (Wed, 10 May 2023) |
| EllapsedTime: 209.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: snpStats.Rcheck |
| Warnings: 2 |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:snpStats.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings snpStats_1.51.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/snpStats.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* 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 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘snpStats/DESCRIPTION’ ... OK
* this is package ‘snpStats’ version ‘1.51.0’
* 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 ‘snpStats’ can be installed ... WARNING
Found the following significant warnings:
readped.c:234:33: warning: ‘%d’ directive output may be truncated writing between 1 and 11 bytes into a region of size between 0 and 127 [-Wformat-truncation=]
testBig.c:31:27: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=]
See ‘/home/biocbuild/bbs-3.17-bioc/meat/snpStats.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
installed size is 6.1Mb
sub-directories of 1Mb or more:
data 4.1Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ... OK
* 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-devel_2023-03-12_r83975-bin/site-library/snpStats/libs/snpStats.so’:
Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
Found ‘rand’, possibly from ‘rand’ (C)
File ‘snpStats/libs/snpStats.so’:
Found non-API call to R: ‘R_data_class’
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.
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘Fst-vignette.Rnw’... OK
‘data-input-vignette.Rnw’... OK
‘differences.Rnw’... OK
‘imputation-vignette.Rnw’... OK
‘ld-vignette.Rnw’... OK
‘pca-vignette.Rnw’... OK
‘snpStats-vignette.Rnw’... OK
‘tdt-vignette.Rnw’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/snpStats.Rcheck/00check.log’
for details.
snpStats.Rcheck/00install.out
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL snpStats
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’
* installing *source* package ‘snpStats’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c Runcertain.c -o Runcertain.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c bind.c -o bind.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c count_gt.c -o count_gt.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c covwin.c -o covwin.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c force_hom.c -o force_hom.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c fst.c -o fst.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c glm_test.c -o glm_test.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c glm_test_R.c -o glm_test_R.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c hash_index.c -o hash_index.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c hphase.c -o hphase.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c imputation.c -o imputation.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c in.c -o in.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c input.c -o input.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c invert.c -o invert.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c ipf.c -o ipf.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c ld.c -o ld.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c misc.c -o misc.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c mla.c -o mla.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c mvphenotype.c -o mvphenotype.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c outdata.c -o outdata.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c plink.c -o plink.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c read_uncertain.c -o read_uncertain.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c readped.c -o readped.o
readped.c: In function ‘readped’:
readped.c:234:33: warning: ‘%d’ directive output may be truncated writing between 1 and 11 bytes into a region of size between 0 and 127 [-Wformat-truncation=]
234 | snprintf(fmid, MAX_ID, "%s%c%d", fid, sepchar, memi);
| ^~
In file included from /usr/include/stdio.h:894,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include/R.h:44,
from readped.c:3:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:71:10: note: ‘__builtin___snprintf_chk’ output between 3 and 140 bytes into a destination of size 128
71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c single_snp_tests.c -o single_snp_tests.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c snp_summary.c -o snp_summary.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c snpmpy.c -o snpmpy.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c solve_cubic.c -o solve_cubic.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c structure.c -o structure.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c subset.c -o subset.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c switch.c -o switch.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c tdt.c -o tdt.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c testBig.c -o testBig.o
testBig.c: In function ‘snp_big’:
testBig.c:31:27: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=]
31 | sprintf(name, "Subject%d", i+1);
| ^~
testBig.c:31:19: note: directive argument in the range [1, 2147483647]
31 | sprintf(name, "Subject%d", i+1);
| ^~~~~~~~~~~
In file included from /usr/include/stdio.h:894,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include/R.h:44,
from testBig.c:1:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 9 and 18 bytes into a destination of size 16
38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
39 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
40 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c uncertain.c -o uncertain.o
gcc -shared -L/usr/local/lib -o snpStats.so Runcertain.o bind.o count_gt.o covwin.o force_hom.o fst.o glm_test.o glm_test_R.o hash_index.o hphase.o imputation.o in.o input.o invert.o ipf.o ld.o misc.o mla.o mvphenotype.o outdata.o plink.o read_uncertain.o readped.o single_snp_tests.o snp_summary.o snpmpy.o solve_cubic.o structure.o subset.o switch.o tdt.o testBig.o uncertain.o -lz
installing to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/00LOCK-snpStats/00new/snpStats/libs
** R
** data
** 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 (snpStats)
snpStats.Rcheck/snpStats-Ex.timings
| name | user | system | elapsed | |
| Fst | 0.487 | 0.016 | 0.503 | |
| GlmEstimates-class | 0.001 | 0.000 | 0.001 | |
| GlmTests-class | 0.001 | 0.000 | 0.001 | |
| ImputationRules-class | 0 | 0 | 0 | |
| SingleSnpTests-class | 0 | 0 | 0 | |
| SnpMatrix-class | 0.171 | 0.019 | 0.190 | |
| XSnpMatrix-class | 0.083 | 0.004 | 0.087 | |
| chi.squared | 0.069 | 0.004 | 0.073 | |
| families | 0.02 | 0.00 | 0.02 | |
| filter.rules | 0 | 0 | 0 | |
| for.exercise | 1.079 | 0.028 | 1.107 | |
| ibsCount | 0.497 | 0.012 | 0.509 | |
| ibsDist | 0.312 | 0.004 | 0.316 | |
| imputation.maf | 0 | 0 | 0 | |
| impute.snps | 0.604 | 0.016 | 0.620 | |
| ld | 0.066 | 0.008 | 0.073 | |
| mean2g | 0.076 | 0.000 | 0.076 | |
| misinherits | 0.041 | 0.012 | 0.053 | |
| mvtests | 0 | 0 | 0 | |
| plotUncertainty | 0 | 0 | 0 | |
| pool | 0.206 | 0.004 | 0.210 | |
| pp | 0.064 | 0.000 | 0.065 | |
| qq.chisq | 0.001 | 0.000 | 0.000 | |
| random.snps | 0.004 | 0.000 | 0.004 | |
| read.beagle | 0 | 0 | 0 | |
| read.impute | 0 | 0 | 0 | |
| read.long | 0 | 0 | 0 | |
| read.mach | 0 | 0 | 0 | |
| read.pedfile | 0 | 0 | 0 | |
| row.summary | 0.124 | 0.004 | 0.127 | |
| single.snp.tests | 0.094 | 0.004 | 0.097 | |
| sm.compare | 0 | 0 | 0 | |
| snp.cor | 0.525 | 0.008 | 0.534 | |
| snp.imputation | 0.581 | 0.032 | 0.613 | |
| snp.lhs.estimates | 0.214 | 0.004 | 0.219 | |
| snp.lhs.tests | 0.081 | 0.000 | 0.082 | |
| snp.pre.multiply | 0.087 | 0.004 | 0.091 | |
| snp.rhs.estimates | 0.095 | 0.016 | 0.111 | |
| snp.rhs.tests | 0.071 | 0.004 | 0.075 | |
| switch.alleles | 0.075 | 0.004 | 0.079 | |
| tdt.snp | 0.015 | 0.004 | 0.020 | |
| test.allele.switch | 0.099 | 0.016 | 0.116 | |
| testdata | 0.124 | 0.012 | 0.136 | |
| write.plink | 0.119 | 0.004 | 0.122 | |
| xxt | 0.456 | 0.012 | 0.468 | |