Guenter Klambauer
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/cn.mops |
| Branch: master |
| Last Commit: e8b02c3 |
| Last Changed Date: 2018-10-30 11:54:30 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:26:43 -0400 (Tue, 09 Apr 2019).
| Package 295/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| cn.mops 1.29.0 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 | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
| Package: cn.mops |
| Version: 1.29.0 |
| 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_1.29.0.tar.gz |
| StartedAt: 2019-04-08 23:58:36 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-09 00:02:56 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 260.2 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_1.29.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/cn.mops.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.29.0’
* 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 13.575 0.050 26.846
calcFractionalCopyNumbers-CNVDetectionResult-method 10.547 0.078 10.736
calcFractionalCopyNumbers 10.368 0.045 10.532
cn.mops 9.453 0.189 26.398
haplocn.mops 1.503 0.041 14.705
getReadCountsFromBAM 0.637 0.015 7.236
getSegmentReadCountsFromBAM 0.383 0.011 6.748
* 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’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 -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 -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/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
* DONE (cn.mops)
cn.mops.Rcheck/cn.mops-Ex.timings
| name | user | system | elapsed | |
| CNVDetectionResult | 0.001 | 0.000 | 0.002 | |
| calcFractionalCopyNumbers-CNVDetectionResult-method | 10.547 | 0.078 | 10.736 | |
| calcFractionalCopyNumbers | 10.368 | 0.045 | 10.532 | |
| calcIntegerCopyNumbers-CNVDetectionResult-method | 0.602 | 0.012 | 0.633 | |
| calcIntegerCopyNumbers | 0.506 | 0.012 | 0.524 | |
| cn.mops | 9.453 | 0.189 | 26.398 | |
| cnvr-CNVDetectionResult-method | 0.291 | 0.010 | 0.305 | |
| cnvr | 0.636 | 0.017 | 0.660 | |
| cnvs-CNVDetectionResult-method | 0.282 | 0.009 | 0.294 | |
| cnvs | 0.294 | 0.007 | 0.306 | |
| exomecn.mops | 4.261 | 0.034 | 4.341 | |
| getReadCountsFromBAM | 0.637 | 0.015 | 7.236 | |
| getSegmentReadCountsFromBAM | 0.383 | 0.011 | 6.748 | |
| gr-CNVDetectionResult-method | 0.293 | 0.008 | 0.304 | |
| gr | 0.290 | 0.008 | 0.303 | |
| haplocn.mops | 1.503 | 0.041 | 14.705 | |
| individualCall-CNVDetectionResult-method | 0.320 | 0.006 | 0.329 | |
| individualCall | 0.310 | 0.006 | 0.319 | |
| iniCall-CNVDetectionResult-method | 0.317 | 0.007 | 0.324 | |
| iniCall | 0.290 | 0.006 | 0.298 | |
| integerCopyNumber-CNVDetectionResult-method | 0.307 | 0.008 | 0.316 | |
| integerCopyNumber | 0.304 | 0.007 | 0.312 | |
| localAssessments-CNVDetectionResult-method | 0.308 | 0.005 | 0.316 | |
| localAssessments | 0.299 | 0.006 | 0.311 | |
| makeRobustCNVR | 0.508 | 0.006 | 0.524 | |
| normalizeChromosomes | 0.604 | 0.019 | 0.632 | |
| normalizeGenome | 0.908 | 0.014 | 0.928 | |
| normalizedData-CNVDetectionResult-method | 0.318 | 0.008 | 0.326 | |
| normalizedData | 0.303 | 0.008 | 0.312 | |
| params-CNVDetectionResult-method | 0.303 | 0.013 | 0.321 | |
| params | 0.257 | 0.013 | 0.272 | |
| posteriorProbs-CNVDetectionResult-method | 0.286 | 0.006 | 0.296 | |
| posteriorProbs | 0.270 | 0.007 | 0.278 | |
| referencecn.mops | 13.575 | 0.050 | 26.846 | |
| sampleNames-CNVDetectionResult-method | 0.297 | 0.008 | 0.306 | |
| sampleNames | 0.294 | 0.007 | 0.303 | |
| segment | 0.029 | 0.000 | 0.029 | |
| segmentation-CNVDetectionResult-method | 0.310 | 0.007 | 0.324 | |
| segmentation | 0.281 | 0.007 | 0.293 | |
| segplot-CNVDetectionResult-method | 1.285 | 0.008 | 1.304 | |
| segplot | 1.251 | 0.009 | 1.273 | |
| singlecn.mops | 1.182 | 0.010 | 1.206 | |