Tulip Nandu
| Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 May 2024) |
| git_url: https://git.bioconductor.org/packages/groHMM |
| git_branch: RELEASE_3_19 |
| git_last_commit: bc510e7 |
| git_last_commit_date: 2024-04-30 10:40:02 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.19 |
|
This page was generated on 2024-05-07 11:32:35 -0400 (Tue, 07 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
| 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 | ||||
| Package 917/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| groHMM 1.38.0 (landing page) Tulip Nandu
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the groHMM package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: groHMM |
| Version: 1.38.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:groHMM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings groHMM_1.38.0.tar.gz |
| StartedAt: 2024-05-06 22:03:27 -0400 (Mon, 06 May 2024) |
| EndedAt: 2024-05-06 22:04:45 -0400 (Mon, 06 May 2024) |
| EllapsedTime: 77.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: groHMM.Rcheck |
| Warnings: 1 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:groHMM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings groHMM_1.38.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/groHMM.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘groHMM/DESCRIPTION’ ... OK
* this is package ‘groHMM’ version ‘1.38.0’
* 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 ... WARNING
Found the following significant warnings:
hmmMiscFunctions.c:236:49: warning: format specifies type 'int' but the argument has type 'double' [-Wformat]
See ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/groHMM.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 code 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/groHMM.Rcheck/00check.log’
for details.
groHMM.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL groHMM
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘groHMM’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c AnnotateProbes.c -o AnnotateProbes.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c DecayAlgorithm.c -o DecayAlgorithm.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MLEfit.c -o MLEfit.o
MLEfit.c:260:25: warning: variable 'cnt' set but not used [-Wunused-but-set-variable]
int maxn = 2*n_x+1, cnt=0;
^
In file included from MLEfit.c:43:
./hmmHeader.h:281:16: warning: unused function 'MargainalizeSumLogProbOver' [-Wunused-function]
static double MargainalizeSumLogProbOver(int state, int position,
^
./hmmHeader.h:301:16: warning: unused function 'expSum' [-Wunused-function]
static double expSum(double *logValues, int length) {
^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RegisterRRoutines.c -o RegisterRRoutines.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Windowing.c -o Windowing.o
Windowing.c:146:6: warning: unused variable 'II' [-Wunused-variable]
int II = 0;
^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hmmEM.c -o hmmEM.o
In file included from hmmEM.c:50:
./hmmHeader.h:281:16: warning: unused function 'MargainalizeSumLogProbOver' [-Wunused-function]
static double MargainalizeSumLogProbOver(int state, int position,
^
./hmmHeader.h:301:16: warning: unused function 'expSum' [-Wunused-function]
static double expSum(double *logValues, int length) {
^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hmmFwBw.c -o hmmFwBw.o
In file included from hmmFwBw.c:45:
./hmmHeader.h:281:16: warning: unused function 'MargainalizeSumLogProbOver' [-Wunused-function]
static double MargainalizeSumLogProbOver(int state, int position,
^
./hmmHeader.h:301:16: warning: unused function 'expSum' [-Wunused-function]
static double expSum(double *logValues, int length) {
^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hmmMiscFunctions.c -o hmmMiscFunctions.o
hmmMiscFunctions.c:236:49: warning: format specifies type 'int' but the argument has type 'double' [-Wformat]
Assertion about to fail! logPP= %d\n", logPP);
~~ ^~~~~
%f
hmmMiscFunctions.c:384:10: warning: unused variable 'wi' [-Wunused-variable]
double wi, *newEx;
^
hmmMiscFunctions.c:417:10: warning: unused variable 'epsilon' [-Wunused-variable]
double epsilon=0.00001;
^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hmmViterbi.c -o hmmViterbi.o
In file included from hmmViterbi.c:48:
./hmmHeader.h:281:16: warning: unused function 'MargainalizeSumLogProbOver' [-Wunused-function]
static double MargainalizeSumLogProbOver(int state, int position,
^
./hmmHeader.h:301:16: warning: unused function 'expSum' [-Wunused-function]
static double expSum(double *logValues, int length) {
^
2 warnings generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o groHMM.so AnnotateProbes.o DecayAlgorithm.o MLEfit.o RegisterRRoutines.o Windowing.o hmmEM.o hmmFwBw.o hmmMiscFunctions.o hmmViterbi.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 | 0.135 | 0.008 | 0.143 | |
| combineTranscripts | 0.061 | 0.005 | 0.066 | |
| detectTranscripts | 0.109 | 0.004 | 0.114 | |
| evaluateHMMInAnnotations | 0.317 | 0.002 | 0.319 | |
| getCores | 0 | 0 | 0 | |
| getTxDensity | 0.004 | 0.000 | 0.004 | |
| limitToXkb | 0.016 | 0.000 | 0.016 | |
| makeConsensusAnnotations | 0 | 0 | 0 | |
| metaGene | 0.022 | 0.000 | 0.023 | |
| pausingIndex | 0.072 | 0.004 | 0.075 | |
| polymeraseWave | 0.188 | 0.016 | 0.205 | |
| runMetaGene | 0.004 | 0.000 | 0.004 | |
| windowAnalysis | 0.071 | 0.005 | 0.076 | |
| writeWiggle | 0.071 | 0.003 | 0.074 | |