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BioC 3.6: CHECK report for cn.mops on veracruz1

This page was generated on 2017-08-16 13:42:34 -0400 (Wed, 16 Aug 2017).

Package 245/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.mops 1.23.0
Guenter Klambauer
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cn.mops
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: cn.mops
Version: 1.23.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cn.mops_1.23.0.tar.gz
StartedAt: 2017-08-16 01:19:11 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:23:38 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 267.5 seconds
RetCode: 0
Status:  OK 
CheckDir: cn.mops.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cn.mops_1.23.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/cn.mops.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.23.0’
* 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 loading without being on the library search path ... 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                                      user system elapsed
referencecn.mops                                    10.771  0.047  23.600
calcFractionalCopyNumbers-CNVDetectionResult-method 10.414  0.088  13.357
calcFractionalCopyNumbers                            9.350  0.042  11.990
cn.mops                                              7.949  0.119  26.947
haplocn.mops                                         1.994  0.028  16.932
getReadCountsFromBAM                                 0.985  0.011   9.369
getSegmentReadCountsFromBAM                          0.301  0.007   8.234
* 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: OK

cn.mops.Rcheck/00install.out:

* 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:228:15: 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 /Users/biocbuild/bbs-3.6-bioc/meat/cn.mops.Rcheck/cn.mops/libs
** R
** data
** inst
** preparing 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:

nameusersystemelapsed
CNVDetectionResult0.0010.0000.002
calcFractionalCopyNumbers-CNVDetectionResult-method10.414 0.08813.357
calcFractionalCopyNumbers 9.350 0.04211.990
calcIntegerCopyNumbers-CNVDetectionResult-method0.6890.0070.871
calcIntegerCopyNumbers1.0930.0071.383
cn.mops 7.949 0.11926.947
cnvr-CNVDetectionResult-method0.2570.0070.339
cnvr0.2430.0050.321
cnvs-CNVDetectionResult-method0.2560.0050.324
cnvs0.2580.0050.332
exomecn.mops3.5830.0334.555
getReadCountsFromBAM0.9850.0119.369
getSegmentReadCountsFromBAM0.3010.0078.234
gr-CNVDetectionResult-method0.2780.0090.285
gr0.2660.0100.318
haplocn.mops 1.994 0.02816.932
individualCall-CNVDetectionResult-method0.2690.0090.319
individualCall0.5200.0160.682
iniCall-CNVDetectionResult-method0.2790.0100.332
iniCall0.2490.0130.282
integerCopyNumber-CNVDetectionResult-method0.2630.0090.293
integerCopyNumber0.2520.0090.271
localAssessments-CNVDetectionResult-method0.2590.0110.285
localAssessments0.2620.0130.286
makeRobustCNVR0.3630.0110.386
normalizeChromosomes0.2800.0240.319
normalizeGenome0.2890.0150.306
normalizedData-CNVDetectionResult-method0.2560.0070.271
normalizedData0.2260.0070.235
params-CNVDetectionResult-method0.2140.0140.234
params0.2230.0140.243
posteriorProbs-CNVDetectionResult-method0.2480.0120.268
posteriorProbs0.2370.0090.254
referencecn.mops10.771 0.04723.600
sampleNames-CNVDetectionResult-method0.2010.0090.220
sampleNames0.1850.0090.193
segment0.0240.0000.023
segmentation-CNVDetectionResult-method0.2200.0080.239
segmentation0.2240.0100.245
segplot-CNVDetectionResult-method1.1480.0211.201
segplot1.3520.0131.395
singlecn.mops0.8990.0110.938