Guenter Klambauer
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/cn.mops |
| Branch: RELEASE_3_7 |
| Last Commit: 2f07225 |
| Last Changed Date: 2018-04-30 10:35:22 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:50:08 -0400 (Wed, 17 Oct 2018).
| Package 269/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| cn.mops 1.26.0 Guenter Klambauer
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: cn.mops |
| Version: 1.26.0 |
| 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_1.26.0.tar.gz |
| StartedAt: 2018-10-16 20:33:17 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 20:37:29 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 251.6 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_1.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/cn.mops.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.26.0’
* 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 13.427 0.051 26.188
calcFractionalCopyNumbers-CNVDetectionResult-method 10.568 0.090 10.734
calcFractionalCopyNumbers 9.726 0.038 9.855
cn.mops 9.546 0.191 25.549
haplocn.mops 1.525 0.029 14.470
getReadCountsFromBAM 0.628 0.014 7.045
getSegmentReadCountsFromBAM 0.361 0.009 6.617
* 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-3.7-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/3.5/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++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c cnmops.cpp -o cnmops.o
clang++ -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++ -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/3.5/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 | 0.004 | 0.000 | 0.004 | |
| calcFractionalCopyNumbers-CNVDetectionResult-method | 10.568 | 0.090 | 10.734 | |
| calcFractionalCopyNumbers | 9.726 | 0.038 | 9.855 | |
| calcIntegerCopyNumbers-CNVDetectionResult-method | 0.499 | 0.007 | 0.512 | |
| calcIntegerCopyNumbers | 0.414 | 0.008 | 0.423 | |
| cn.mops | 9.546 | 0.191 | 25.549 | |
| cnvr-CNVDetectionResult-method | 0.320 | 0.007 | 0.333 | |
| cnvr | 0.579 | 0.015 | 0.595 | |
| cnvs-CNVDetectionResult-method | 0.317 | 0.006 | 0.324 | |
| cnvs | 0.285 | 0.004 | 0.292 | |
| exomecn.mops | 4.520 | 0.035 | 4.602 | |
| getReadCountsFromBAM | 0.628 | 0.014 | 7.045 | |
| getSegmentReadCountsFromBAM | 0.361 | 0.009 | 6.617 | |
| gr-CNVDetectionResult-method | 0.331 | 0.008 | 0.342 | |
| gr | 0.309 | 0.005 | 0.316 | |
| haplocn.mops | 1.525 | 0.029 | 14.470 | |
| individualCall-CNVDetectionResult-method | 0.329 | 0.004 | 0.337 | |
| individualCall | 0.323 | 0.005 | 0.330 | |
| iniCall-CNVDetectionResult-method | 0.313 | 0.005 | 0.320 | |
| iniCall | 0.337 | 0.005 | 0.343 | |
| integerCopyNumber-CNVDetectionResult-method | 0.322 | 0.006 | 0.332 | |
| integerCopyNumber | 0.318 | 0.006 | 0.328 | |
| localAssessments-CNVDetectionResult-method | 0.329 | 0.006 | 0.340 | |
| localAssessments | 0.339 | 0.006 | 0.347 | |
| makeRobustCNVR | 0.459 | 0.006 | 0.470 | |
| normalizeChromosomes | 0.648 | 0.030 | 0.683 | |
| normalizeGenome | 0.628 | 0.016 | 0.652 | |
| normalizedData-CNVDetectionResult-method | 0.334 | 0.009 | 0.344 | |
| normalizedData | 0.313 | 0.008 | 0.339 | |
| params-CNVDetectionResult-method | 0.233 | 0.012 | 0.247 | |
| params | 0.311 | 0.013 | 0.326 | |
| posteriorProbs-CNVDetectionResult-method | 0.316 | 0.005 | 0.325 | |
| posteriorProbs | 0.321 | 0.005 | 0.330 | |
| referencecn.mops | 13.427 | 0.051 | 26.188 | |
| sampleNames-CNVDetectionResult-method | 0.311 | 0.007 | 0.323 | |
| sampleNames | 0.302 | 0.005 | 0.310 | |
| segment | 0.036 | 0.001 | 0.038 | |
| segmentation-CNVDetectionResult-method | 0.309 | 0.005 | 0.315 | |
| segmentation | 0.311 | 0.005 | 0.319 | |
| segplot-CNVDetectionResult-method | 1.373 | 0.007 | 1.393 | |
| segplot | 1.353 | 0.008 | 1.374 | |
| singlecn.mops | 1.223 | 0.012 | 1.242 | |