| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:42 -0000 (Wed, 01 Mar 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" | 4266 |
| 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 groHMM package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/groHMM.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 852/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| groHMM 1.33.0 (landing page) Tulip Nandu
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: groHMM |
| Version: 1.33.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:groHMM.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings groHMM_1.33.0.tar.gz |
| StartedAt: 2023-02-28 05:12:52 -0000 (Tue, 28 Feb 2023) |
| EndedAt: 2023-02-28 05:20:37 -0000 (Tue, 28 Feb 2023) |
| EllapsedTime: 465.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: groHMM.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:groHMM.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings groHMM_1.33.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/groHMM.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 ‘groHMM/DESCRIPTION’ ... OK
* this is package ‘groHMM’ version ‘1.33.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'MASS', 'parallel', 'S4Vectors', 'IRanges', 'GenomeInfoDb',
'GenomicRanges', 'GenomicAlignments', 'rtracklayer'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘groHMM’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives no person with maintainer role, valid email
address and non-empty name.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* 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 ...
‘groHMM.Rnw’... OK
OK
* checking re-building of vignette outputs ... NOTE
Warnings in re-building vignettes:
Warning: file stem ‘/home/biocbuild/bbs-3.17-bioc/meat/groHMM.Rcheck/vign_test/groHMM/vignettes/groHMM-fig2’ is not portable
Warning: file stem ‘/home/biocbuild/bbs-3.17-bioc/meat/groHMM.Rcheck/vign_test/groHMM/vignettes/groHMM-fig3’ is not portable
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/groHMM.Rcheck/00check.log’
for details.
groHMM.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL groHMM
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘groHMM’ ...
** 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/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c AnnotateProbes.c -o AnnotateProbes.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c DecayAlgorithm.c -o DecayAlgorithm.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c MLEfit.c -o MLEfit.o
In file included from MLEfit.c:43:
hmmHeader.h:301:16: warning: ‘expSum’ defined but not used [-Wunused-function]
301 | static double expSum(double *logValues, int length) {
| ^~~~~~
hmmHeader.h:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not used [-Wunused-function]
281 | static double MargainalizeSumLogProbOver(int state, int position,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c RegisterRRoutines.c -o RegisterRRoutines.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c Windowing.c -o Windowing.o
Windowing.c: In function ‘WindowAnalysis’:
Windowing.c:146:13: warning: unused variable ‘II’ [-Wunused-variable]
146 | int II = 0;
| ^~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c hmmEM.c -o hmmEM.o
In file included from hmmEM.c:50:
hmmHeader.h:301:16: warning: ‘expSum’ defined but not used [-Wunused-function]
301 | static double expSum(double *logValues, int length) {
| ^~~~~~
hmmHeader.h:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not used [-Wunused-function]
281 | static double MargainalizeSumLogProbOver(int state, int position,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from hmmHeader.h:36,
from hmmEM.c:50:
UsefulValues.h:39:15: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used [-Wunused-variable]
39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20;
| ^~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c hmmFwBw.c -o hmmFwBw.o
hmmFwBw.c: In function ‘forward’:
hmmFwBw.c:142:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
142 | for(k=1; k<n; k++)
| ^~~
hmmFwBw.c:145:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
145 | for (k = 0; k<n; k++) {
| ^~~
In file included from hmmFwBw.c:45:
At top level:
hmmHeader.h:301:16: warning: ‘expSum’ defined but not used [-Wunused-function]
301 | static double expSum(double *logValues, int length) {
| ^~~~~~
hmmHeader.h:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not used [-Wunused-function]
281 | static double MargainalizeSumLogProbOver(int state, int position,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from hmmHeader.h:36,
from hmmFwBw.c:45:
UsefulValues.h:39:15: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used [-Wunused-variable]
39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20;
| ^~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c hmmMiscFunctions.c -o hmmMiscFunctions.o
hmmMiscFunctions.c: In function ‘SStatsNormExp’:
hmmMiscFunctions.c:384:10: warning: unused variable ‘wi’ [-Wunused-variable]
384 | double wi, *newEx;
| ^~
hmmMiscFunctions.c: In function ‘UpdateNormExp’:
hmmMiscFunctions.c:417:10: warning: unused variable ‘epsilon’ [-Wunused-variable]
417 | double epsilon=0.00001;
| ^~~~~~~
In file included from hmmHeader.h:36,
from hmmMiscFunctions.c:43:
At top level:
UsefulValues.h:39:15: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used [-Wunused-variable]
39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20;
| ^~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c hmmViterbi.c -o hmmViterbi.o
In file included from hmmViterbi.c:48:
hmmHeader.h:301:16: warning: ‘expSum’ defined but not used [-Wunused-function]
301 | static double expSum(double *logValues, int length) {
| ^~~~~~
hmmHeader.h:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not used [-Wunused-function]
281 | static double MargainalizeSumLogProbOver(int state, int position,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from hmmHeader.h:36,
from hmmViterbi.c:48:
UsefulValues.h:39:15: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used [-Wunused-variable]
39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20;
| ^~~~~~~~~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o groHMM.so AnnotateProbes.o DecayAlgorithm.o MLEfit.o RegisterRRoutines.o Windowing.o hmmEM.o hmmFwBw.o hmmMiscFunctions.o hmmViterbi.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-groHMM/00new/groHMM/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 (groHMM)
groHMM.Rcheck/groHMM-Ex.timings
| name | user | system | elapsed | |
| breakTranscriptsOnGenes | 0.572 | 0.044 | 0.616 | |
| combineTranscripts | 0.315 | 0.040 | 0.355 | |
| detectTranscripts | 0.345 | 0.035 | 0.382 | |
| evaluateHMMInAnnotations | 0.133 | 0.000 | 0.133 | |
| getCores | 0 | 0 | 0 | |
| getTxDensity | 0.022 | 0.000 | 0.022 | |
| limitToXkb | 0.086 | 0.000 | 0.087 | |
| makeConsensusAnnotations | 0.000 | 0.000 | 0.001 | |
| metaGene | 0.123 | 0.000 | 0.123 | |
| pausingIndex | 0.341 | 0.000 | 0.341 | |
| polymeraseWave | 1.479 | 0.032 | 1.513 | |
| runMetaGene | 0.02 | 0.00 | 0.02 | |
| windowAnalysis | 0.287 | 0.012 | 0.300 | |
| writeWiggle | 0.288 | 0.000 | 0.287 | |