Back to the "Multiple platform build/check report" A  B [C] D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.0: CHECK report for cn.mops on zin1

This page was generated on 2015-04-10 09:39:41 -0700 (Fri, 10 Apr 2015).

Package 172/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.mops 1.12.0
Guenter Klambauer
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/cn.mops
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: cn.mops
Version: 1.12.0
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings cn.mops_1.12.0.tar.gz
StartedAt: 2015-04-09 22:43:55 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 22:48:34 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 278.3 seconds
RetCode: 0
Status:  OK 
CheckDir: cn.mops.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings cn.mops_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/cn.mops.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.12.0’
* 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 ... [14s/14s] 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 ‘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 ‘reduce’
normalizeChromosomes: no visible global function definition for
  ‘seqnames’
normalizeChromosomes: 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 ‘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<-’
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [84s/138s] OK
Examples with CPU or elapsed time > 5s
                                                      user system elapsed
referencecn.mops                                    19.601  0.056  32.488
cn.mops                                             12.709  0.100  28.758
calcFractionalCopyNumbers-CNVDetectionResult-method 12.649  0.036  12.708
calcFractionalCopyNumbers                           12.024  0.008  12.322
haplocn.mops                                         1.664  0.044  14.874
getReadCountsFromBAM                                 0.180  0.024   6.330
getSegmentReadCountsFromBAM                          0.064  0.024   5.489
* 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/cn.mops.Rcheck/00check.log’
for details.

cn.mops.Rcheck/00install.out:

* installing *source* package ‘cn.mops’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_cnmops.c -o R_init_cnmops.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c cnmops.cpp -o cnmops.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c segment.cpp -o segment.o
segment.cpp: In function ‘SEXPREC* segment(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
segment.cpp:59:20: warning: variable ‘globalSd’ set but not used [-Wunused-but-set-variable]
segment.cpp:60:9: warning: variable ‘oldStatistic’ set but not used [-Wunused-but-set-variable]
segment.cpp:61:31: warning: variable ‘maxStatistic’ set but not used [-Wunused-but-set-variable]
segment.cpp:62:40: warning: variable ‘maxIdx’ set but not used [-Wunused-but-set-variable]
segment.cpp:64:9: warning: unused variable ‘Rf_beta’ [-Wunused-variable]
g++ -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-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
CNVDetectionResult0.0000.0000.001
calcFractionalCopyNumbers-CNVDetectionResult-method12.649 0.03612.708
calcFractionalCopyNumbers12.024 0.00812.322
calcIntegerCopyNumbers-CNVDetectionResult-method0.6440.0000.642
calcIntegerCopyNumbers0.4440.0040.449
cn.mops12.709 0.10028.758
cnvr-CNVDetectionResult-method0.2760.0000.279
cnvr0.2840.0040.291
cnvs-CNVDetectionResult-method0.4680.0160.481
cnvs0.2640.0080.272
exomecn.mops4.2850.0044.318
getReadCountsFromBAM0.1800.0246.330
getSegmentReadCountsFromBAM0.0640.0245.489
gr-CNVDetectionResult-method0.3760.0200.398
gr0.3400.0000.342
haplocn.mops 1.664 0.04414.874
individualCall-CNVDetectionResult-method0.3120.0120.371
individualCall0.340.000.34
iniCall-CNVDetectionResult-method0.3040.0040.305
iniCall0.3280.0000.329
integerCopyNumber-CNVDetectionResult-method0.3520.0000.350
integerCopyNumber0.3080.0040.313
localAssessments-CNVDetectionResult-method0.3080.0040.314
localAssessments0.4960.0200.516
makeRobustCNVR0.4840.0080.492
normalizeChromosomes0.3640.0120.377
normalizeGenome0.3400.0000.341
normalizedData-CNVDetectionResult-method0.3000.0000.301
normalizedData0.3080.0000.309
params-CNVDetectionResult-method0.3120.0040.318
params0.3040.0000.322
posteriorProbs-CNVDetectionResult-method0.2760.0000.277
posteriorProbs0.3000.0000.299
referencecn.mops19.601 0.05632.488
sampleNames-CNVDetectionResult-method0.3080.0160.323
sampleNames0.2720.0040.273
segment0.0280.0000.029
segmentation-CNVDetectionResult-method0.3040.0040.309
segmentation0.3080.0000.308
segplot-CNVDetectionResult-method1.3850.0041.389
segplot1.3440.0041.350
singlecn.mops1.1480.0041.154