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BioC 3.1: CHECK report for cn.mops on zin2

This page was generated on 2015-10-09 09:24:47 -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: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings cn.mops_1.14.1.tar.gz
StartedAt: 2015-10-08 23:41:58 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:46:51 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 293.0 seconds
RetCode: 0
Status:  OK 
CheckDir: cn.mops.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings cn.mops_1.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/cn.mops.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.14.1’
* 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 ... [9s/13s] 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 ... [75s/171s] OK
Examples with CPU or elapsed time > 5s
                                                      user system elapsed
referencecn.mops                                    18.852  0.039  40.878
calcFractionalCopyNumbers-CNVDetectionResult-method 12.082  0.019  17.178
calcFractionalCopyNumbers                           11.741  0.011  15.013
cn.mops                                             10.291  0.099  35.955
exomecn.mops                                         4.226  0.015   5.585
haplocn.mops                                         1.602  0.073  18.771
getReadCountsFromBAM                                 0.150  0.023   7.277
getSegmentReadCountsFromBAM                          0.050  0.034   6.498
* 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-3.1-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-3.1-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-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c cnmops.cpp -o cnmops.o
g++ -I/home/biocbuild/bbs-3.1-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-3.1-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-3.1-bioc/R/lib -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/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
CNVDetectionResult0.0010.0000.001
calcFractionalCopyNumbers-CNVDetectionResult-method12.082 0.01917.178
calcFractionalCopyNumbers11.741 0.01115.013
calcIntegerCopyNumbers-CNVDetectionResult-method0.4140.0000.832
calcIntegerCopyNumbers0.5620.0000.807
cn.mops10.291 0.09935.955
cnvr-CNVDetectionResult-method0.2730.0080.288
cnvr0.2630.0070.517
cnvs-CNVDetectionResult-method0.2780.0000.374
cnvs0.2810.0040.346
exomecn.mops4.2260.0155.585
getReadCountsFromBAM0.1500.0237.277
getSegmentReadCountsFromBAM0.0500.0346.498
gr-CNVDetectionResult-method0.3140.0040.502
gr0.3000.0000.537
haplocn.mops 1.602 0.07318.771
individualCall-CNVDetectionResult-method0.3080.0000.308
individualCall0.2940.0040.406
iniCall-CNVDetectionResult-method0.2830.0040.386
iniCall0.2920.0000.507
integerCopyNumber-CNVDetectionResult-method0.2950.0000.492
integerCopyNumber0.2830.0110.439
localAssessments-CNVDetectionResult-method0.3000.0000.399
localAssessments0.2840.0040.309
makeRobustCNVR0.4030.0000.505
normalizeChromosomes0.3350.0000.553
normalizeGenome0.3110.0040.348
normalizedData-CNVDetectionResult-method0.2950.0000.420
normalizedData0.2950.0000.387
params-CNVDetectionResult-method0.2720.0080.466
params0.2710.0040.340
posteriorProbs-CNVDetectionResult-method0.2680.0000.309
posteriorProbs0.2670.0000.441
referencecn.mops18.852 0.03940.878
sampleNames-CNVDetectionResult-method0.2690.0160.441
sampleNames0.2670.0000.267
segment0.0250.0000.025
segmentation-CNVDetectionResult-method0.2840.0040.288
segmentation0.2980.0030.497
segplot-CNVDetectionResult-method1.1670.0041.677
segplot1.1700.0041.902
singlecn.mops0.9610.0041.550