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BioC 3.1: CHECK report for cn.mops on petty

This page was generated on 2015-10-09 09:34:51 -0700 (Fri, 09 Oct 2015).

Package 183/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.mops 1.14.1
Guenter Klambauer
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/cn.mops
Last Changed Rev: 106320 / Revision: 109384
Last Changed Date: 2015-07-14 00:46:50 -0700 (Tue, 14 Jul 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  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: 1.14.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cn.mops_1.14.1.tar.gz
StartedAt: 2015-10-08 22:10:21 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 22:16:23 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 361.2 seconds
RetCode: 0
Status:  OK 
CheckDir: cn.mops.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cn.mops_1.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/cn.mops.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.14.1’
* 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 ... [19s/19s] 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 ... NOTE
'library' or 'require' call to ‘DNAcopy’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Biobase’ ‘BiocGenerics’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.convertToFastSegRes: no visible global function definition for
  ‘subjectHits’
.convertToFastSegRes: no visible global function definition for
  ‘values<-’
.makeLogRatios: no visible global function definition for ‘rowMedians’
.makeLogRatios: no visible global function definition for ‘values<-’
.replaceNames: no visible global function definition for ‘values<-’
.segPlot: no visible global function definition for ‘seqnames’
.segPlot: no visible global function definition for ‘ranges’
cn.mops: no visible global function definition for ‘strand’
cn.mops: no visible global function definition for ‘seqnames’
cn.mops: no visible global function definition for ‘GRanges’
cn.mops: no visible global function definition for ‘seqinfo’
cn.mops: no visible global function definition for ‘sortSeqlevels’
cn.mops: no visible global function definition for ‘isUnique’
cn.mops: no visible global function definition for ‘reduce’
cn.mops: no visible global function definition for ‘values<-’
getReadCountsFromBAM: no visible global function definition for
  ‘sortSeqlevels’
getReadCountsFromBAM: no visible global function definition for
  ‘seqlengths<-’
getReadCountsFromBAM: no visible global function definition for
  ‘seqlevels’
haplocn.mops: no visible global function definition for ‘strand’
haplocn.mops: no visible global function definition for ‘seqnames’
haplocn.mops: no visible global function definition for ‘GRanges’
haplocn.mops: no visible global function definition for ‘seqinfo’
haplocn.mops: no visible global function definition for ‘sortSeqlevels’
haplocn.mops: no visible global function definition for ‘isUnique’
haplocn.mops: no visible global function definition for ‘reduce’
normalizeChromosomes: no visible global function definition for
  ‘seqnames’
normalizeChromosomes: no visible global function definition for
  ‘values<-’
normalizeGenome: no visible global function definition for ‘values<-’
referencecn.mops: no visible global function definition for ‘strand’
referencecn.mops: no visible global function definition for ‘seqnames’
referencecn.mops: no visible global function definition for ‘GRanges’
referencecn.mops: no visible global function definition for ‘seqinfo’
referencecn.mops: no visible global function definition for
  ‘sortSeqlevels’
referencecn.mops: no visible global function definition for ‘isUnique’
referencecn.mops: no visible global function definition for ‘reduce’
referencecn.mops: no visible global function definition for ‘values<-’
singlecn.mops: no visible global function definition for ‘GRanges’
singlecn.mops: no visible global function definition for ‘strand’
singlecn.mops: no visible global function definition for ‘seqnames’
singlecn.mops: no visible global function definition for ‘seqinfo’
singlecn.mops: no visible global function definition for
  ‘sortSeqlevels’
calcIntegerCopyNumbers,CNVDetectionResult: no visible global function
  definition for ‘values<-’
individualCall,CNVDetectionResult: no visible global function
  definition for ‘values<-’
iniCall,CNVDetectionResult: no visible global function definition for
  ‘values<-’
integerCopyNumber,CNVDetectionResult: no visible global function
  definition for ‘values<-’
localAssessments,CNVDetectionResult: no visible global function
  definition for ‘values<-’
makeRobustCNVR,CNVDetectionResult: no visible global function
  definition for ‘seqnames’
makeRobustCNVR,CNVDetectionResult: no visible global function
  definition for ‘GRanges’
makeRobustCNVR,CNVDetectionResult: no visible global function
  definition for ‘values<-’
makeRobustCNVR,CNVDetectionResult: no visible global function
  definition for ‘reduce’
normalizedData,CNVDetectionResult: no visible global function
  definition for ‘values<-’
plot,CNVDetectionResult-missing : .local: no visible global function
  definition for ‘GRanges’
plot,CNVDetectionResult-missing : .local: no visible global function
  definition for ‘seqnames’
plot,CNVDetectionResult-missing : .local: no visible global function
  definition for ‘rowMedians’
segplot,CNVDetectionResult: no visible global function definition for
  ‘sampleNames’
* 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 ... [104s/176s] OK
Examples with CPU or elapsed time > 5s
                                                      user system elapsed
referencecn.mops                                    20.937  0.045  38.574
cn.mops                                             15.122  0.211  36.383
calcFractionalCopyNumbers-CNVDetectionResult-method 15.189  0.106  15.304
calcFractionalCopyNumbers                           13.946  0.030  13.981
exomecn.mops                                         5.987  0.060   6.048
haplocn.mops                                         2.495  0.033  19.408
getReadCountsFromBAM                                 0.282  0.013   8.383
getSegmentReadCountsFromBAM                          0.106  0.006   7.625
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/cn.mops.Rcheck/00check.log’
for details.


cn.mops.Rcheck/00install.out:

* installing *source* package ‘cn.mops’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_init_cnmops.c -o R_init_cnmops.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c cnmops.cpp -o cnmops.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c segment.cpp -o segment.o
segment.cpp: In function ‘SEXPREC* segment(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
segment.cpp:64: warning: unused variable ‘Rf_beta’
llvm-g++-4.2 -arch x86_64 -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 -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-3.1-bioc/meat/cn.mops.Rcheck/cn.mops/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (cn.mops)

cn.mops.Rcheck/cn.mops-Ex.timings:

nameusersystemelapsed
CNVDetectionResult0.0040.0000.004
calcFractionalCopyNumbers-CNVDetectionResult-method15.189 0.10615.304
calcFractionalCopyNumbers13.946 0.03013.981
calcIntegerCopyNumbers-CNVDetectionResult-method0.7320.0080.741
calcIntegerCopyNumbers0.9710.0080.980
cn.mops15.122 0.21136.383
cnvr-CNVDetectionResult-method0.4440.0120.456
cnvr0.4600.0110.471
cnvs-CNVDetectionResult-method0.5590.0090.567
cnvs0.5630.0080.573
exomecn.mops5.9870.0606.048
getReadCountsFromBAM0.2820.0138.383
getSegmentReadCountsFromBAM0.1060.0067.625
gr-CNVDetectionResult-method0.5870.0180.606
gr0.5090.0120.522
haplocn.mops 2.495 0.03319.408
individualCall-CNVDetectionResult-method0.5890.0130.604
individualCall0.8250.0170.843
iniCall-CNVDetectionResult-method0.5120.0090.521
iniCall0.5390.0100.548
integerCopyNumber-CNVDetectionResult-method0.4920.0090.501
integerCopyNumber0.4920.0090.501
localAssessments-CNVDetectionResult-method0.4930.0090.502
localAssessments0.4940.0090.503
makeRobustCNVR0.6980.0090.707
normalizeChromosomes0.5380.0510.589
normalizeGenome0.7600.0170.777
normalizedData-CNVDetectionResult-method0.4370.0100.447
normalizedData0.5170.0100.527
params-CNVDetectionResult-method0.4880.0170.506
params0.4730.0150.489
posteriorProbs-CNVDetectionResult-method0.4590.0070.466
posteriorProbs0.4680.0080.476
referencecn.mops20.937 0.04538.574
sampleNames-CNVDetectionResult-method0.4510.0080.459
sampleNames0.5290.0080.538
segment0.0520.0000.052
segmentation-CNVDetectionResult-method0.9390.0250.967
segmentation0.5440.0090.554
segplot-CNVDetectionResult-method2.0220.0132.034
segplot2.1160.0132.131
singlecn.mops1.6940.0191.714