Guenter Klambauer
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/cn.mops |
| Branch: RELEASE_3_8 |
| Last Commit: f953d10 |
| Last Changed Date: 2018-10-30 11:41:48 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:56:11 -0400 (Tue, 16 Apr 2019).
| Package 285/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| cn.mops 1.28.0 Guenter Klambauer
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: cn.mops |
| Version: 1.28.0 |
| 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_1.28.0.tar.gz |
| StartedAt: 2019-04-15 23:04:41 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 23:08:58 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 257.3 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_1.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/cn.mops.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.28.0’
* 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 13.972 0.044 27.256
calcFractionalCopyNumbers-CNVDetectionResult-method 10.714 0.090 10.894
calcFractionalCopyNumbers 10.586 0.042 10.750
cn.mops 9.543 0.199 25.924
haplocn.mops 1.522 0.029 14.521
getReadCountsFromBAM 0.906 0.015 7.225
getSegmentReadCountsFromBAM 0.373 0.011 6.492
* 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-3.8-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 | 0.002 | 0.001 | 0.002 | |
| calcFractionalCopyNumbers-CNVDetectionResult-method | 10.714 | 0.090 | 10.894 | |
| calcFractionalCopyNumbers | 10.586 | 0.042 | 10.750 | |
| calcIntegerCopyNumbers-CNVDetectionResult-method | 0.507 | 0.007 | 0.518 | |
| calcIntegerCopyNumbers | 0.459 | 0.006 | 0.472 | |
| cn.mops | 9.543 | 0.199 | 25.924 | |
| cnvr-CNVDetectionResult-method | 0.344 | 0.009 | 0.355 | |
| cnvr | 0.320 | 0.009 | 0.333 | |
| cnvs-CNVDetectionResult-method | 0.641 | 0.014 | 0.662 | |
| cnvs | 0.288 | 0.010 | 0.300 | |
| exomecn.mops | 4.212 | 0.033 | 4.277 | |
| getReadCountsFromBAM | 0.906 | 0.015 | 7.225 | |
| getSegmentReadCountsFromBAM | 0.373 | 0.011 | 6.492 | |
| gr-CNVDetectionResult-method | 0.302 | 0.008 | 0.312 | |
| gr | 0.293 | 0.009 | 0.303 | |
| haplocn.mops | 1.522 | 0.029 | 14.521 | |
| individualCall-CNVDetectionResult-method | 0.314 | 0.009 | 0.327 | |
| individualCall | 0.323 | 0.009 | 0.333 | |
| iniCall-CNVDetectionResult-method | 0.308 | 0.009 | 0.320 | |
| iniCall | 0.321 | 0.010 | 0.335 | |
| integerCopyNumber-CNVDetectionResult-method | 0.312 | 0.010 | 0.324 | |
| integerCopyNumber | 0.313 | 0.008 | 0.323 | |
| localAssessments-CNVDetectionResult-method | 0.320 | 0.010 | 0.335 | |
| localAssessments | 0.295 | 0.010 | 0.306 | |
| makeRobustCNVR | 0.468 | 0.009 | 0.479 | |
| normalizeChromosomes | 0.591 | 0.023 | 0.620 | |
| normalizeGenome | 0.624 | 0.017 | 0.645 | |
| normalizedData-CNVDetectionResult-method | 0.324 | 0.007 | 0.333 | |
| normalizedData | 0.330 | 0.005 | 0.343 | |
| params-CNVDetectionResult-method | 0.311 | 0.015 | 0.328 | |
| params | 0.352 | 0.014 | 0.368 | |
| posteriorProbs-CNVDetectionResult-method | 0.314 | 0.008 | 0.327 | |
| posteriorProbs | 0.282 | 0.006 | 0.294 | |
| referencecn.mops | 13.972 | 0.044 | 27.256 | |
| sampleNames-CNVDetectionResult-method | 0.302 | 0.006 | 0.313 | |
| sampleNames | 0.295 | 0.005 | 0.303 | |
| segment | 0.029 | 0.000 | 0.030 | |
| segmentation-CNVDetectionResult-method | 0.311 | 0.006 | 0.321 | |
| segmentation | 0.312 | 0.006 | 0.319 | |
| segplot-CNVDetectionResult-method | 1.373 | 0.008 | 1.424 | |
| segplot | 1.361 | 0.008 | 1.386 | |
| singlecn.mops | 1.247 | 0.010 | 1.275 | |