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BioC 3.4: CHECK report for cn.mops on morelia

This page was generated on 2017-04-15 16:23:55 -0400 (Sat, 15 Apr 2017).

Package 226/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.mops 1.20.1
Guenter Klambauer
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/cn.mops
Last Changed Rev: 127614 / Revision: 128728
Last Changed Date: 2017-03-22 08:51:06 -0400 (Wed, 22 Mar 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
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: cn.mops
Version: 1.20.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cn.mops_1.20.1.tar.gz
StartedAt: 2017-04-15 00:05:04 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 00:08:49 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 225.5 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_1.20.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/cn.mops.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.20.1’
* 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                                    10.170  0.027  20.145
cn.mops                                              9.350  0.144  23.127
calcFractionalCopyNumbers                            8.098  0.029   8.131
calcFractionalCopyNumbers-CNVDetectionResult-method  7.917  0.054   7.977
haplocn.mops                                         1.660  0.019  12.799
getReadCountsFromBAM                                 0.399  0.017   5.650
getSegmentReadCountsFromBAM                          0.282  0.010   5.776
* 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 -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -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 -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c cnmops.cpp -o cnmops.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -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:230:15: 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-3.4-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
CNVDetectionResult0.0020.0000.001
calcFractionalCopyNumbers-CNVDetectionResult-method7.9170.0547.977
calcFractionalCopyNumbers8.0980.0298.131
calcIntegerCopyNumbers-CNVDetectionResult-method0.3760.0070.383
calcIntegerCopyNumbers0.5820.0090.591
cn.mops 9.350 0.14423.127
cnvr-CNVDetectionResult-method0.2930.0110.305
cnvr0.3000.0050.306
cnvs-CNVDetectionResult-method0.3070.0080.314
cnvs0.3050.0080.314
exomecn.mops3.8120.0603.874
getReadCountsFromBAM0.3990.0175.650
getSegmentReadCountsFromBAM0.2820.0105.776
gr-CNVDetectionResult-method0.3230.0070.330
gr0.3510.0060.357
haplocn.mops 1.660 0.01912.799
individualCall-CNVDetectionResult-method0.2940.0070.300
individualCall0.3220.0060.327
iniCall-CNVDetectionResult-method0.3070.0060.312
iniCall0.3350.0050.341
integerCopyNumber-CNVDetectionResult-method0.2840.0040.289
integerCopyNumber0.3120.0060.318
localAssessments-CNVDetectionResult-method0.2980.0060.304
localAssessments0.3090.0050.314
makeRobustCNVR0.4920.0180.510
normalizeChromosomes0.3280.0190.348
normalizeGenome0.3350.0080.345
normalizedData-CNVDetectionResult-method0.2900.0050.295
normalizedData0.3150.0050.335
params-CNVDetectionResult-method0.2530.0150.323
params0.2820.0120.294
posteriorProbs-CNVDetectionResult-method0.3060.0060.312
posteriorProbs0.2750.0050.303
referencecn.mops10.170 0.02720.145
sampleNames-CNVDetectionResult-method0.3200.0060.327
sampleNames0.3160.0050.321
segment0.0300.0010.030
segmentation-CNVDetectionResult-method0.2930.0050.298
segmentation0.3260.0110.338
segplot-CNVDetectionResult-method1.3470.0091.357
segplot1.4030.0101.413
singlecn.mops0.9290.0080.937