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BioC 3.2: CHECK report for iChip on zin1

This page was generated on 2015-08-24 10:47:44 -0700 (Mon, 24 Aug 2015).

Package 500/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iChip 1.23.0
Qianxing Mo
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/iChip
Last Changed Rev: 102594 / Revision: 107696
Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  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: iChip
Version: 1.23.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings iChip_1.23.0.tar.gz
StartedAt: 2015-08-24 00:50:53 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 00:51:23 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 29.4 seconds
RetCode: 0
Status:  OK 
CheckDir: iChip.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings iChip_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/iChip.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 ‘iChip/DESCRIPTION’ ... OK
* this is package ‘iChip’ version ‘1.23.0’
* 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 ‘iChip’ can be installed ... [2s/2s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [13s/13s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
iChip2 6.523      0   6.548
iChip1 5.909      0   5.930
* 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

iChip.Rcheck/00install.out:

* installing *source* package ‘iChip’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c iChip.c -o iChip.o
iChip.c: In function ‘iChip2’:
iChip.c:24:69: warning: unused variable ‘sdsignal’ [-Wunused-variable]
   double *score2,z0,z1,p,meanScore,varScore,sdScore,mean3sd,sdnoise,sdsignal;
                                                                     ^
iChip.c:24:61: warning: unused variable ‘sdnoise’ [-Wunused-variable]
   double *score2,z0,z1,p,meanScore,varScore,sdScore,mean3sd,sdnoise,sdsignal;
                                                             ^
iChip.c:23:51: warning: variable ‘nrowm1’ set but not used [-Wunused-but-set-variable]
   int sampleSize,LB,RB,i,j,r,nnoise,nsignal,state,nrowm1,wtsum;
                                                   ^
iChip.c: In function ‘iChip1’:
iChip.c:188:20: warning: unused variable ‘j’ [-Wunused-variable]
   int sampleSize,i,j,r,nnoise,nsignal,state,nrowm1,sumxx,rm1;
                    ^
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o iChip.so iChip.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/iChip.Rcheck/iChip/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (iChip)

iChip.Rcheck/iChip-Ex.timings:

nameusersystemelapsed
enrichreg0.0110.0000.011
iChip15.9090.0005.930
iChip26.5230.0006.548
lmtstat0.2460.0000.246