Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-09 21:30 -0500 (Sat, 09 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4505 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4486 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 386/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cn.mops 1.52.0 (landing page) Gundula Povysil
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the cn.mops package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cn.mops.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: cn.mops |
Version: 1.52.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cn.mops_1.52.0.tar.gz |
StartedAt: 2024-11-08 23:10:12 -0500 (Fri, 08 Nov 2024) |
EndedAt: 2024-11-08 23:14:57 -0500 (Fri, 08 Nov 2024) |
EllapsedTime: 284.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: cn.mops.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cn.mops_1.52.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/cn.mops.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘cn.mops/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘cn.mops’ version ‘1.52.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘cn.mops’ can be installed ... OK * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * 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 ... OK * 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 whether startup messages can be suppressed ... 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 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed referencecn.mops 2.591 0.016 5.619 cn.mops 1.684 0.044 5.290 * 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 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/cn.mops.Rcheck/00check.log’ for details.
cn.mops.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cn.mops ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘cn.mops’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ 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 R_init_cnmops.c -o R_init_cnmops.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cnmops.cpp -o cnmops.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c segment.cpp -o segment.o segment.cpp:59:20: warning: variable 'globalSd' set but not used [-Wunused-but-set-variable] double globalMean,globalSd,diff,M2,globalVariance; ^ segment.cpp:60:9: warning: variable 'oldStatistic' set but not used [-Wunused-but-set-variable] double oldStatistic, meanLeft,meanRight,varLeft,varRight; ^ segment.cpp:61:31: warning: variable 'maxStatistic' set but not used [-Wunused-but-set-variable] double newStatistic,meanDiff,maxStatistic,DOF,a,b,eps1; ^ segment.cpp:62:40: warning: variable 'maxIdx' set but not used [-Wunused-but-set-variable] double newPValue, maxPValue,oldPValue,maxIdx; ^ segment.cpp:64:9: warning: unused variable 'Rf_beta' [-Wunused-variable] double beta,nn; ^ /Library/Frameworks/R.framework/Resources/include/Rmath.h:210:15: note: expanded from macro 'beta' #define beta Rf_beta ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.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-cn.mops/00new/cn.mops/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 (cn.mops)
cn.mops.Rcheck/cn.mops-Ex.timings
name | user | system | elapsed | |
CNVDetectionResult | 0.000 | 0.000 | 0.001 | |
calcFractionalCopyNumbers-CNVDetectionResult-method | 1.901 | 0.009 | 1.911 | |
calcFractionalCopyNumbers | 1.868 | 0.011 | 1.881 | |
calcIntegerCopyNumbers-CNVDetectionResult-method | 0.120 | 0.001 | 0.121 | |
calcIntegerCopyNumbers | 0.106 | 0.002 | 0.107 | |
cn.mops | 1.684 | 0.044 | 5.290 | |
cnvr-CNVDetectionResult-method | 0.062 | 0.002 | 0.065 | |
cnvr | 0.058 | 0.001 | 0.060 | |
cnvs-CNVDetectionResult-method | 0.061 | 0.001 | 0.062 | |
cnvs | 0.058 | 0.001 | 0.059 | |
exomecn.mops | 0.646 | 0.010 | 0.656 | |
getReadCountsFromBAM | 0.119 | 0.010 | 1.632 | |
getSegmentReadCountsFromBAM | 0.069 | 0.005 | 1.601 | |
gr-CNVDetectionResult-method | 0.064 | 0.001 | 0.066 | |
gr | 0.059 | 0.001 | 0.060 | |
haplocn.mops | 0.265 | 0.013 | 3.267 | |
individualCall-CNVDetectionResult-method | 0.060 | 0.001 | 0.061 | |
individualCall | 0.061 | 0.001 | 0.062 | |
iniCall-CNVDetectionResult-method | 0.059 | 0.001 | 0.060 | |
iniCall | 0.064 | 0.001 | 0.064 | |
integerCopyNumber-CNVDetectionResult-method | 0.059 | 0.001 | 0.060 | |
integerCopyNumber | 0.062 | 0.001 | 0.063 | |
localAssessments-CNVDetectionResult-method | 0.063 | 0.001 | 0.064 | |
localAssessments | 0.059 | 0.001 | 0.061 | |
makeRobustCNVR | 0.100 | 0.002 | 0.102 | |
normalizeChromosomes | 0.052 | 0.005 | 0.057 | |
normalizeGenome | 0.054 | 0.005 | 0.060 | |
normalizedData-CNVDetectionResult-method | 0.060 | 0.000 | 0.061 | |
normalizedData | 0.063 | 0.001 | 0.064 | |
params-CNVDetectionResult-method | 0.057 | 0.003 | 0.061 | |
params | 0.181 | 0.008 | 0.189 | |
posteriorProbs-CNVDetectionResult-method | 0.057 | 0.001 | 0.057 | |
posteriorProbs | 0.057 | 0.001 | 0.057 | |
referencecn.mops | 2.591 | 0.016 | 5.619 | |
sampleNames-CNVDetectionResult-method | 0.064 | 0.003 | 0.066 | |
sampleNames | 0.061 | 0.001 | 0.061 | |
segment | 0.006 | 0.000 | 0.006 | |
segmentation-CNVDetectionResult-method | 0.061 | 0.001 | 0.063 | |
segmentation | 0.058 | 0.002 | 0.058 | |
segplot-CNVDetectionResult-method | 0.240 | 0.001 | 0.241 | |
segplot | 0.245 | 0.002 | 0.246 | |
singlecn.mops | 0.196 | 0.002 | 0.198 | |