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BioC 3.2: CHECK report for cn.mops on zin1

This page was generated on 2016-04-23 10:12:16 -0700 (Sat, 23 Apr 2016).

Package 191/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.mops 1.16.2
Guenter Klambauer
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/cn.mops
Last Changed Rev: 111631 / Revision: 116712
Last Changed Date: 2015-12-18 04:32:14 -0800 (Fri, 18 Dec 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca 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: 1.16.2
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings cn.mops_1.16.2.tar.gz
StartedAt: 2016-04-22 23:17:18 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 23:20:46 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 208.6 seconds
RetCode: 0
Status:  OK 
CheckDir: cn.mops.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings cn.mops_1.16.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/cn.mops.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-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 ‘1.16.2’
* 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 ... [10s/10s] 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.
Package in Depends field not imported from: ‘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<-’
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 ‘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 ... [74s/112s] OK
Examples with CPU or elapsed time > 5s
                                                      user system elapsed
referencecn.mops                                    18.190  0.045  26.770
calcFractionalCopyNumbers-CNVDetectionResult-method 11.734  0.024  11.778
calcFractionalCopyNumbers                           11.344  0.000  11.346
cn.mops                                             10.267  0.120  22.491
haplocn.mops                                         1.437  0.060  10.514
* 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
  ‘/home/biocbuild/bbs-3.2-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-3.2-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-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c cnmops.cpp -o cnmops.o
g++ -I/home/biocbuild/bbs-3.2-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]
  double globalMean,globalSd,diff,M2,globalVariance;
                    ^
segment.cpp:60:9: warning: variable ‘oldStatistic’ set but not used [-Wunused-but-set-variable]
  double oldStatistic, meanLeft,meanRight,varLeft,varRight;
         ^
segment.cpp:61:31: warning: variable ‘maxStatistic’ set but not used [-Wunused-but-set-variable]
  double newStatistic,meanDiff,maxStatistic,DOF,a,b,eps1;
                               ^
segment.cpp:62:40: warning: variable ‘maxIdx’ set but not used [-Wunused-but-set-variable]
  double newPValue, maxPValue,oldPValue,maxIdx;
                                        ^
In file included from segment.cpp:10:0:
/home/biocbuild/bbs-3.2-bioc/R/include/Rmath.h:217:15: warning: unused variable ‘Rf_beta’ [-Wunused-variable]
 #define beta  Rf_beta
               ^
segment.cpp:64:9: note: in expansion of macro ‘beta’
  double beta,nn;
         ^
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-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-method11.734 0.02411.778
calcFractionalCopyNumbers11.344 0.00011.346
calcIntegerCopyNumbers-CNVDetectionResult-method0.5710.0040.580
calcIntegerCopyNumbers0.3620.0000.362
cn.mops10.267 0.12022.491
cnvr-CNVDetectionResult-method0.2580.0120.273
cnvr0.2650.0000.264
cnvs-CNVDetectionResult-method0.2660.0000.266
cnvs0.2800.0040.284
exomecn.mops4.0820.0124.095
getReadCountsFromBAM0.1510.0164.534
getSegmentReadCountsFromBAM0.0630.0233.953
gr-CNVDetectionResult-method0.2880.0160.303
gr0.3180.0080.326
haplocn.mops 1.437 0.06010.514
individualCall-CNVDetectionResult-method0.5310.0160.547
individualCall0.2890.0040.293
iniCall-CNVDetectionResult-method0.2780.0000.278
iniCall0.2820.0000.281
integerCopyNumber-CNVDetectionResult-method0.2800.0040.285
integerCopyNumber0.2840.0000.283
localAssessments-CNVDetectionResult-method0.2840.0000.282
localAssessments0.2840.0000.284
makeRobustCNVR0.3880.0000.389
normalizeChromosomes0.2890.0080.296
normalizeGenome0.4870.0040.491
normalizedData-CNVDetectionResult-method0.2720.0000.273
normalizedData0.2840.0000.283
params-CNVDetectionResult-method0.2650.0040.269
params0.2680.0040.272
posteriorProbs-CNVDetectionResult-method0.2580.0000.258
posteriorProbs0.2590.0000.266
referencecn.mops18.190 0.04526.770
sampleNames-CNVDetectionResult-method0.3130.0120.325
sampleNames0.2790.0040.283
segment0.0250.0000.025
segmentation-CNVDetectionResult-method0.2610.0040.264
segmentation0.2680.0000.268
segplot-CNVDetectionResult-method1.2240.0001.223
segplot1.3030.0121.320
singlecn.mops0.8860.0080.893