Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-29 11:37:36 -0400 (Fri, 29 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
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 380/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cn.mops 1.48.0 (landing page) Gundula Povysil
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.48.0 |
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_1.48.0.tar.gz |
StartedAt: 2024-03-28 00:51:19 -0400 (Thu, 28 Mar 2024) |
EndedAt: 2024-03-28 00:58:45 -0400 (Thu, 28 Mar 2024) |
EllapsedTime: 446.1 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_1.48.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/cn.mops.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * 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 ‘1.48.0’ * 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 ‘cn.mops’ can be installed ... OK * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * 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 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 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 14.390 0.115 36.435 cn.mops 12.314 0.276 42.682 calcFractionalCopyNumbers-CNVDetectionResult-method 11.994 0.142 14.708 calcFractionalCopyNumbers 11.695 0.101 14.701 exomecn.mops 5.514 0.065 6.680 haplocn.mops 2.233 0.059 24.378 getReadCountsFromBAM 0.942 0.027 11.400 getSegmentReadCountsFromBAM 0.570 0.018 10.561 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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-3.18-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/4.3-x86_64/Resources/library’ * installing *source* package ‘cn.mops’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_cnmops.c -o R_init_cnmops.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cnmops.cpp -o cnmops.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c segment.cpp -o segment.o 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:59:20: warning: variable 'globalSd' set but not used [-Wunused-but-set-variable] double globalMean,globalSd,diff,M2,globalVariance; ^ 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 ^ segment.cpp:60:9: warning: variable 'oldStatistic' set but not used [-Wunused-but-set-variable] double oldStatistic, meanLeft,meanRight,varLeft,varRight; ^ segment.cpp:62:40: warning: variable 'maxIdx' set but not used [-Wunused-but-set-variable] double newPValue, maxPValue,oldPValue,maxIdx; ^ 5 warnings generated. clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/4.3-x86_64/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 | 0.002 | 0.002 | 0.004 | |
calcFractionalCopyNumbers-CNVDetectionResult-method | 11.994 | 0.142 | 14.708 | |
calcFractionalCopyNumbers | 11.695 | 0.101 | 14.701 | |
calcIntegerCopyNumbers-CNVDetectionResult-method | 0.858 | 0.011 | 1.024 | |
calcIntegerCopyNumbers | 0.804 | 0.016 | 0.979 | |
cn.mops | 12.314 | 0.276 | 42.682 | |
cnvr-CNVDetectionResult-method | 0.462 | 0.014 | 0.564 | |
cnvr | 0.444 | 0.007 | 0.548 | |
cnvs-CNVDetectionResult-method | 0.452 | 0.008 | 0.572 | |
cnvs | 0.446 | 0.008 | 0.557 | |
exomecn.mops | 5.514 | 0.065 | 6.680 | |
getReadCountsFromBAM | 0.942 | 0.027 | 11.400 | |
getSegmentReadCountsFromBAM | 0.570 | 0.018 | 10.561 | |
gr-CNVDetectionResult-method | 0.452 | 0.007 | 0.477 | |
gr | 0.456 | 0.008 | 0.485 | |
haplocn.mops | 2.233 | 0.059 | 24.378 | |
individualCall-CNVDetectionResult-method | 0.475 | 0.010 | 0.516 | |
individualCall | 0.477 | 0.010 | 0.566 | |
iniCall-CNVDetectionResult-method | 0.495 | 0.008 | 0.557 | |
iniCall | 0.479 | 0.009 | 0.556 | |
integerCopyNumber-CNVDetectionResult-method | 0.465 | 0.009 | 0.522 | |
integerCopyNumber | 0.479 | 0.009 | 0.516 | |
localAssessments-CNVDetectionResult-method | 0.853 | 0.018 | 0.921 | |
localAssessments | 0.464 | 0.009 | 0.502 | |
makeRobustCNVR | 0.799 | 0.008 | 0.868 | |
normalizeChromosomes | 0.379 | 0.013 | 0.415 | |
normalizeGenome | 0.371 | 0.013 | 0.415 | |
normalizedData-CNVDetectionResult-method | 0.473 | 0.017 | 0.532 | |
normalizedData | 0.468 | 0.010 | 0.526 | |
params-CNVDetectionResult-method | 0.440 | 0.036 | 0.518 | |
params | 0.453 | 0.037 | 0.537 | |
posteriorProbs-CNVDetectionResult-method | 0.437 | 0.007 | 0.488 | |
posteriorProbs | 0.438 | 0.007 | 0.476 | |
referencecn.mops | 14.390 | 0.115 | 36.435 | |
sampleNames-CNVDetectionResult-method | 0.445 | 0.010 | 0.475 | |
sampleNames | 0.441 | 0.007 | 0.478 | |
segment | 0.041 | 0.001 | 0.045 | |
segmentation-CNVDetectionResult-method | 0.437 | 0.009 | 0.479 | |
segmentation | 0.453 | 0.009 | 0.502 | |
segplot-CNVDetectionResult-method | 1.983 | 0.014 | 2.191 | |
segplot | 2.023 | 0.018 | 2.303 | |
singlecn.mops | 1.745 | 0.024 | 1.879 | |