Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-01-16 13:34:19 -0500 (Thu, 16 Jan 2020).
Package 316/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
cn.mops 1.33.0 Guenter Klambauer
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
Package: cn.mops |
Version: 1.33.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cn.mops_1.33.0.tar.gz |
StartedAt: 2020-01-16 03:00:40 -0500 (Thu, 16 Jan 2020) |
EndedAt: 2020-01-16 03:07:02 -0500 (Thu, 16 Jan 2020) |
EllapsedTime: 381.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: cn.mops.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cn.mops_1.33.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/cn.mops.Rcheck’ * using R Under development (unstable) (2019-12-14 r77572) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * 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 ‘1.33.0’ * 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 * 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 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 14.221 0.083 35.348 cn.mops 11.753 0.377 38.648 calcFractionalCopyNumbers-CNVDetectionResult-method 11.844 0.128 12.068 calcFractionalCopyNumbers 11.526 0.061 11.678 exomecn.mops 5.260 0.085 5.415 haplocn.mops 2.303 0.062 23.668 getReadCountsFromBAM 0.983 0.027 10.688 getSegmentReadCountsFromBAM 0.683 0.026 10.930 * 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-3.11-bioc/meat/cn.mops.Rcheck/00check.log’ for details.
cn.mops.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL cn.mops ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘cn.mops’ ... ** using staged installation ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c R_init_cnmops.c -o R_init_cnmops.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c cnmops.cpp -o cnmops.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c segment.cpp -o segment.o segment.cpp:64:9: warning: unused variable 'Rf_beta' [-Wunused-variable] double beta,nn; ^ /Library/Frameworks/R.framework/Resources/include/Rmath.h:212:15: note: expanded from macro 'beta' #define beta Rf_beta ^ 1 warning generated. clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/4.0/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 | 0.001 | 0.003 | |
calcFractionalCopyNumbers-CNVDetectionResult-method | 11.844 | 0.128 | 12.068 | |
calcFractionalCopyNumbers | 11.526 | 0.061 | 11.678 | |
calcIntegerCopyNumbers-CNVDetectionResult-method | 0.945 | 0.014 | 0.975 | |
calcIntegerCopyNumbers | 0.917 | 0.023 | 0.989 | |
cn.mops | 11.753 | 0.377 | 38.648 | |
cnvr-CNVDetectionResult-method | 0.465 | 0.015 | 0.480 | |
cnvr | 0.445 | 0.010 | 0.461 | |
cnvs-CNVDetectionResult-method | 0.485 | 0.010 | 0.517 | |
cnvs | 0.464 | 0.010 | 0.491 | |
exomecn.mops | 5.260 | 0.085 | 5.415 | |
getReadCountsFromBAM | 0.983 | 0.027 | 10.688 | |
getSegmentReadCountsFromBAM | 0.683 | 0.026 | 10.930 | |
gr-CNVDetectionResult-method | 0.486 | 0.015 | 0.504 | |
gr | 0.484 | 0.014 | 0.516 | |
haplocn.mops | 2.303 | 0.062 | 23.668 | |
individualCall-CNVDetectionResult-method | 0.485 | 0.014 | 0.499 | |
individualCall | 0.510 | 0.015 | 0.526 | |
iniCall-CNVDetectionResult-method | 0.399 | 0.014 | 0.412 | |
iniCall | 0.466 | 0.012 | 0.480 | |
integerCopyNumber-CNVDetectionResult-method | 0.473 | 0.011 | 0.484 | |
integerCopyNumber | 0.511 | 0.015 | 0.526 | |
localAssessments-CNVDetectionResult-method | 0.432 | 0.014 | 0.451 | |
localAssessments | 0.487 | 0.013 | 0.499 | |
makeRobustCNVR | 1.377 | 0.028 | 1.412 | |
normalizeChromosomes | 0.365 | 0.033 | 0.399 | |
normalizeGenome | 0.383 | 0.044 | 0.429 | |
normalizedData-CNVDetectionResult-method | 0.497 | 0.022 | 0.520 | |
normalizedData | 0.495 | 0.015 | 0.524 | |
params-CNVDetectionResult-method | 0.490 | 0.030 | 0.531 | |
params | 0.472 | 0.029 | 0.502 | |
posteriorProbs-CNVDetectionResult-method | 0.464 | 0.009 | 0.474 | |
posteriorProbs | 0.422 | 0.008 | 0.431 | |
referencecn.mops | 14.221 | 0.083 | 35.348 | |
sampleNames-CNVDetectionResult-method | 0.447 | 0.010 | 0.458 | |
sampleNames | 0.416 | 0.009 | 0.425 | |
segment | 0.044 | 0.001 | 0.047 | |
segmentation-CNVDetectionResult-method | 0.470 | 0.010 | 0.483 | |
segmentation | 0.429 | 0.009 | 0.442 | |
segplot-CNVDetectionResult-method | 2.002 | 0.018 | 2.066 | |
segplot | 1.952 | 0.012 | 1.970 | |
singlecn.mops | 1.644 | 0.020 | 1.667 | |