Guenter Klambauer
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/cn.mops |
| Branch: RELEASE_3_9 |
| Last Commit: a17073a |
| Last Changed Date: 2019-05-02 11:53:33 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:49:39 -0400 (Wed, 16 Oct 2019).
| Package 300/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| cn.mops 1.30.0 Guenter Klambauer
| malbec2 | Linux (Ubuntu 18.04.2 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: 1.30.0 |
| 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_1.30.0.tar.gz |
| StartedAt: 2019-10-16 01:34:49 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 01:40:15 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 326.0 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_1.30.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/cn.mops.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.30.0’
* 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 or elapsed time > 5s
user system elapsed
referencecn.mops 14.051 0.090 31.695
calcFractionalCopyNumbers-CNVDetectionResult-method 11.504 0.155 11.707
calcFractionalCopyNumbers 11.082 0.073 11.261
cn.mops 10.428 0.371 32.132
haplocn.mops 1.772 0.062 19.933
getReadCountsFromBAM 0.790 0.022 8.735
getSegmentReadCountsFromBAM 0.427 0.016 9.135
* 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-3.9-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/3.6/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/3.6/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 | 0.003 | 0.001 | 0.004 | |
| calcFractionalCopyNumbers-CNVDetectionResult-method | 11.504 | 0.155 | 11.707 | |
| calcFractionalCopyNumbers | 11.082 | 0.073 | 11.261 | |
| calcIntegerCopyNumbers-CNVDetectionResult-method | 1.080 | 0.026 | 1.107 | |
| calcIntegerCopyNumbers | 0.623 | 0.013 | 0.635 | |
| cn.mops | 10.428 | 0.371 | 32.132 | |
| cnvr-CNVDetectionResult-method | 0.302 | 0.009 | 0.312 | |
| cnvr | 0.706 | 0.036 | 0.743 | |
| cnvs-CNVDetectionResult-method | 0.337 | 0.013 | 0.350 | |
| cnvs | 0.343 | 0.010 | 0.352 | |
| exomecn.mops | 4.478 | 0.055 | 4.535 | |
| getReadCountsFromBAM | 0.790 | 0.022 | 8.735 | |
| getSegmentReadCountsFromBAM | 0.427 | 0.016 | 9.135 | |
| gr-CNVDetectionResult-method | 0.392 | 0.016 | 0.409 | |
| gr | 0.388 | 0.016 | 0.404 | |
| haplocn.mops | 1.772 | 0.062 | 19.933 | |
| individualCall-CNVDetectionResult-method | 0.353 | 0.015 | 0.368 | |
| individualCall | 0.346 | 0.017 | 0.363 | |
| iniCall-CNVDetectionResult-method | 0.357 | 0.014 | 0.371 | |
| iniCall | 0.351 | 0.014 | 0.365 | |
| integerCopyNumber-CNVDetectionResult-method | 0.372 | 0.016 | 0.389 | |
| integerCopyNumber | 0.388 | 0.016 | 0.404 | |
| localAssessments-CNVDetectionResult-method | 0.315 | 0.013 | 0.329 | |
| localAssessments | 0.368 | 0.011 | 0.379 | |
| makeRobustCNVR | 0.658 | 0.010 | 0.675 | |
| normalizeChromosomes | 0.349 | 0.035 | 0.387 | |
| normalizeGenome | 0.332 | 0.031 | 0.366 | |
| normalizedData-CNVDetectionResult-method | 0.360 | 0.009 | 0.373 | |
| normalizedData | 0.343 | 0.014 | 0.357 | |
| params-CNVDetectionResult-method | 0.330 | 0.025 | 0.355 | |
| params | 0.351 | 0.025 | 0.382 | |
| posteriorProbs-CNVDetectionResult-method | 0.356 | 0.009 | 0.364 | |
| posteriorProbs | 0.324 | 0.008 | 0.331 | |
| referencecn.mops | 14.051 | 0.090 | 31.695 | |
| sampleNames-CNVDetectionResult-method | 0.339 | 0.015 | 0.354 | |
| sampleNames | 0.357 | 0.023 | 0.380 | |
| segment | 0.037 | 0.001 | 0.037 | |
| segmentation-CNVDetectionResult-method | 0.366 | 0.015 | 0.381 | |
| segmentation | 0.252 | 0.018 | 0.272 | |
| segplot-CNVDetectionResult-method | 1.481 | 0.026 | 1.510 | |
| segplot | 1.595 | 0.020 | 1.650 | |
| singlecn.mops | 1.612 | 0.025 | 1.642 | |