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BioC 3.2: CHECK report for cn.farms on zin1

This page was generated on 2016-04-23 10:11:42 -0700 (Sat, 23 Apr 2016).

Package 190/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.farms 1.18.0
Andreas Mitterecker
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.farms
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 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.farms
Version: 1.18.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings cn.farms_1.18.0.tar.gz
StartedAt: 2016-04-22 23:17:10 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 23:19:19 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 128.7 seconds
RetCode: 0
Status:  OK 
CheckDir: cn.farms.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings cn.farms_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/cn.farms.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.farms/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cn.farms’ version ‘1.18.0’
* 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.farms’ can be installed ... [12s/12s] 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 ... NOTE
initializeBigMatrix: no visible global function definition for
  ‘isPackageLoaded’
* 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 R/sysdata.rda ... 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 ... [15s/15s] OK
* 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-3.2-bioc/meat/cn.farms.Rcheck/00check.log’
for details.


cn.farms.Rcheck/00install.out:

* installing *source* package ‘cn.farms’ ...
** 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_cnfarms.c -o R_init_cnfarms.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c laplace.cpp -o laplace.o
laplace.cpp: In function ‘SEXPREC* momentsGauss(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
laplace.cpp:442:6: warning: unused variable ‘method’ [-Wunused-variable]
  int method=0;
      ^
laplace.cpp: In function ‘void computeParameters(double, double, double, double, double, double, int&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&)’:
laplace.cpp:368:56: warning: ‘I1right’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  double rightMoment1=1.0*rightMy*I0right+1.0*rightSigma*I1right;
                                                        ^
laplace.cpp:367:52: warning: ‘I1left’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  double leftMoment1=1.0*leftMy*I0left+1.0*leftSigma*I1left;
                                                    ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c sparse_farms.c -o sparse_farms.o
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o cn.farms.so R_init_cnfarms.o laplace.o sparse_farms.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/cn.farms.Rcheck/cn.farms/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cn.farms)

cn.farms.Rcheck/cn.farms-Ex.timings:

nameusersystemelapsed
cn.farms0.0010.0000.000
combineData0.7770.0240.810
createAnnotation000
distributionDistance0.3260.0080.333
dnaCopySf0.0960.0000.096
fragLengCorr1.9600.0241.982
mlSummarization2.5430.0722.624
normalizeAverage0.0020.0000.002
normalizeCels000
normalizeNpData000
plotDendrogram0.3110.0000.311
plotDensity0.4200.0040.424
plotEvalIc0.3000.0040.303
plotRegions0.3230.0000.323
plotSmoothScatter0.4810.0040.484
plotViolines0.1010.0000.101
slSummarization2.2340.0162.273
sparseFarmsC0.0010.0000.001
summarizeFarmsExact0.0040.0000.005
summarizeFarmsExact20.0050.0000.005
summarizeFarmsExact30.0050.0000.005
summarizeFarmsGaussian0.0020.0000.002
summarizeFarmsMethods0.0020.0000.002
summarizeFarmsVariational0.0000.0040.003
summarizeWindowBps0.0040.0000.005
summarizeWindowMethods0.0020.0000.002
summarizeWindowStd0.0030.0000.003