Guenter Klambauer
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/cn.mops |
| Branch: master |
| Last Commit: 3e791be |
| Last Changed Date: 2019-10-29 13:36:01 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
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 |
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### Running command:
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### /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
###
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* 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
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL cn.mops
###
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* 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 | |