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BioC 3.0: CHECK report for CSSP on zin1

This page was generated on 2015-04-10 09:41:04 -0700 (Fri, 10 Apr 2015).

Package 213/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CSSP 1.5.1
Chandler Zuo
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/CSSP
Last Changed Rev: 99191 / Revision: 102249
Last Changed Date: 2015-02-07 04:18:39 -0800 (Sat, 07 Feb 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: CSSP
Version: 1.5.1
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings CSSP_1.5.1.tar.gz
StartedAt: 2015-04-09 23:02:20 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:03:18 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 58.0 seconds
RetCode: 0
Status:  OK 
CheckDir: CSSP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings CSSP_1.5.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/CSSP.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CSSP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CSSP’ version ‘1.5.1’
* 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 ‘CSSP’ can be installed ... [3s/3s] 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
Namespaces in Imports field not imported from:
  ‘methods’ ‘stats’ ‘utils’
  All declared Imports should be used.
* 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
File ‘CSSP/libs/CSSP.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘gridSample.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘gridSample.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [35s/36s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
cssp.power-methods 27.958  0.072  28.094
cssp.fit-methods    6.044  0.000   6.079
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘run_tests.R’ [3s/4s]
 [4s/4s] 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/CSSP.Rcheck/00check.log’
for details.

CSSP.Rcheck/00install.out:

* installing *source* package ‘CSSP’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c bincount.c -o bincount.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c binpower.c -o binpower.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c gridLogMean.c -o gridLogMean.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c gridMGC.c -o gridMGC.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c gridMean.c -o gridMean.o
gridMean.c: In function ‘gridMGCmean_c’:
gridMean.c:10:63: warning: unused variable ‘counter’ [-Wunused-variable]
gridMean.c: In function ‘gridMmean_c’:
gridMean.c:177:63: warning: unused variable ‘counter’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c gridMode.c -o gridMode.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c gridNonpa.c -o gridNonpa.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c gridSample.c -o gridSample.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c tag2bin.c -o tag2bin.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o CSSP.so bincount.o binpower.o gridLogMean.o gridMGC.o gridMean.o gridMode.o gridNonpa.o gridSample.o tag2bin.o -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-bioc/meat/CSSP.Rcheck/CSSP/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 (CSSP)

CSSP.Rcheck/CSSP-Ex.timings:

nameusersystemelapsed
CSSPFit-class0.0040.0000.002
bindcount0.1440.0040.149
bindcount.chr0.0200.0040.023
callpeak-methods0.0120.0000.014
createBinData0.3080.0040.318
cssp.fit-methods6.0440.0006.079
cssp.power-methods27.958 0.07228.094
cssp.sim-methods0.0160.0080.024
fit.freq-methods0.3400.0000.342
pBBT-methods0.0040.0000.005
peakcount0.1080.0000.106
peakcount.chr0.0120.0040.015
qBBT-methods0.0440.0000.044
readBinFile0.0120.0000.013
tag2bin0.0040.0080.012
tag2bin.chr0.0080.0000.005