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CHECK report for cn.mops on malbec1

This page was generated on 2019-04-16 11:49:27 -0400 (Tue, 16 Apr 2019).

Package 285/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.mops 1.28.0
Guenter Klambauer
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/cn.mops
Branch: RELEASE_3_8
Last Commit: f953d10
Last Changed Date: 2018-10-30 11:41:48 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cn.mops
Version: 1.28.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings cn.mops_1.28.0.tar.gz
StartedAt: 2019-04-15 23:00:22 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:04:12 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 229.9 seconds
RetCode: 0
Status:  OK 
CheckDir: cn.mops.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings cn.mops_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/cn.mops.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.28.0’
* 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 ... 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 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                                      user system elapsed
referencecn.mops                                    13.452  0.104  24.248
calcFractionalCopyNumbers                           11.044  0.008  11.060
calcFractionalCopyNumbers-CNVDetectionResult-method 10.784  0.008  10.817
cn.mops                                              9.920  0.168  25.056
haplocn.mops                                         1.384  0.128  12.790
getReadCountsFromBAM                                 0.800  0.028   6.590
getSegmentReadCountsFromBAM                          0.396  0.068   6.145
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/cn.mops.Rcheck/00check.log’
for details.



Installation output

cn.mops.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL cn.mops
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘cn.mops’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c cnmops.cpp -o cnmops.o
g++  -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include/Rmath.h:212:15: 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-3.8-bioc/R/lib -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/cn.mops/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cn.mops)

Tests output


Example timings

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

nameusersystemelapsed
CNVDetectionResult0.0000.0000.002
calcFractionalCopyNumbers-CNVDetectionResult-method10.784 0.00810.817
calcFractionalCopyNumbers11.044 0.00811.060
calcIntegerCopyNumbers-CNVDetectionResult-method0.5360.0080.543
calcIntegerCopyNumbers0.4560.0000.453
cn.mops 9.920 0.16825.056
cnvr-CNVDetectionResult-method0.3160.0280.344
cnvr0.1880.0080.196
cnvs-CNVDetectionResult-method0.5200.0280.550
cnvs0.1840.0040.192
exomecn.mops2.8560.0002.857
getReadCountsFromBAM0.8000.0286.590
getSegmentReadCountsFromBAM0.3960.0686.145
gr-CNVDetectionResult-method0.3280.0320.365
gr0.3480.0040.354
haplocn.mops 1.384 0.12812.790
individualCall-CNVDetectionResult-method0.3360.0120.349
individualCall0.3320.0080.342
iniCall-CNVDetectionResult-method0.3440.0000.342
iniCall0.3000.0040.306
integerCopyNumber-CNVDetectionResult-method0.2720.0080.281
integerCopyNumber0.3360.0040.339
localAssessments-CNVDetectionResult-method0.2800.0040.285
localAssessments0.1960.0000.194
makeRobustCNVR0.2800.0040.283
normalizeChromosomes0.5960.0200.619
normalizeGenome0.6080.0000.608
normalizedData-CNVDetectionResult-method0.2080.0000.208
normalizedData0.3080.0080.316
params-CNVDetectionResult-method0.2960.0040.301
params0.3040.0080.312
posteriorProbs-CNVDetectionResult-method0.3120.0000.315
posteriorProbs0.2520.0000.256
referencecn.mops13.452 0.10424.248
sampleNames-CNVDetectionResult-method0.2440.0200.268
sampleNames0.3040.0080.313
segment0.0280.0000.029
segmentation-CNVDetectionResult-method0.3200.0000.322
segmentation0.3320.0000.336
segplot-CNVDetectionResult-method0.9560.0080.969
segplot0.8920.0000.893
singlecn.mops0.7120.0040.715