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BioC 3.4: CHECK report for cn.mops on malbec1

This page was generated on 2017-04-15 16:10:43 -0400 (Sat, 15 Apr 2017).

Package 226/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.mops 1.20.1
Guenter Klambauer
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/cn.mops
Last Changed Rev: 127614 / Revision: 128728
Last Changed Date: 2017-03-22 08:51:06 -0400 (Wed, 22 Mar 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  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: 1.20.1
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings cn.mops_1.20.1.tar.gz
StartedAt: 2017-04-14 21:39:40 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 21:42:53 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 192.8 seconds
RetCode: 0
Status:  OK 
CheckDir: cn.mops.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings cn.mops_1.20.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/cn.mops.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.20.1’
* 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 ... 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 ... 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                                      user system elapsed
calcFractionalCopyNumbers-CNVDetectionResult-method 13.356  0.048  13.414
referencecn.mops                                     9.612  0.052  18.808
cn.mops                                              8.076  0.124  18.993
calcFractionalCopyNumbers                            6.808  0.000   6.816
haplocn.mops                                         1.204  0.080  11.579
getReadCountsFromBAM                                 0.296  0.028   5.072
getSegmentReadCountsFromBAM                          0.232  0.048   5.200
* 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: OK

cn.mops.Rcheck/00install.out:

* installing *source* package ‘cn.mops’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c cnmops.cpp -o cnmops.o
g++ -I/home/biocbuild/bbs-3.4-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-3.4-bioc/R/include/Rmath.h:230:15: 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-3.4-bioc/R/lib -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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-method13.356 0.04813.414
calcFractionalCopyNumbers6.8080.0006.816
calcIntegerCopyNumbers-CNVDetectionResult-method0.4920.0000.496
calcIntegerCopyNumbers0.60.00.6
cn.mops 8.076 0.12418.993
cnvr-CNVDetectionResult-method0.2440.0040.247
cnvr0.2160.0040.219
cnvs-CNVDetectionResult-method0.2400.0120.249
cnvs0.220.000.22
exomecn.mops3.3480.0203.371
getReadCountsFromBAM0.2960.0285.072
getSegmentReadCountsFromBAM0.2320.0485.200
gr-CNVDetectionResult-method0.2520.0040.257
gr0.2280.0040.234
haplocn.mops 1.204 0.08011.579
individualCall-CNVDetectionResult-method0.2800.0120.291
individualCall0.2360.0000.235
iniCall-CNVDetectionResult-method0.2320.0000.233
iniCall0.240.000.24
integerCopyNumber-CNVDetectionResult-method0.2480.0000.250
integerCopyNumber0.2280.0040.231
localAssessments-CNVDetectionResult-method0.2280.0000.228
localAssessments0.2400.0000.242
makeRobustCNVR0.3160.0040.321
normalizeChromosomes0.2040.0080.213
normalizeGenome0.2040.0040.208
normalizedData-CNVDetectionResult-method0.2240.0040.228
normalizedData0.4400.0160.458
params-CNVDetectionResult-method0.2120.0000.212
params0.2320.0000.235
posteriorProbs-CNVDetectionResult-method0.2120.0000.209
posteriorProbs0.2160.0000.218
referencecn.mops 9.612 0.05218.808
sampleNames-CNVDetectionResult-method0.3480.0160.366
sampleNames0.3600.0080.370
segment0.0320.0000.034
segmentation-CNVDetectionResult-method0.2640.0000.265
segmentation0.2200.0000.222
segplot-CNVDetectionResult-method0.980.000.98
segplot0.9400.0040.947
singlecn.mops0.7400.0040.747