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BioC 2.13: CHECK report for CSSP on perceval

This page was generated on 2014-04-05 09:53:10 -0700 (Sat, 05 Apr 2014).

Package 179/750HostnameOS / ArchBUILDCHECKBUILD BIN
CSSP 1.1.2
Chandler Zuo
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/CSSP
Last Changed Rev: 87237 / Revision: 88450
Last Changed Date: 2014-03-08 12:31:09 -0800 (Sat, 08 Mar 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: CSSP
Version: 1.1.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CSSP_1.1.2.tar.gz
StartedAt: 2014-04-05 00:38:06 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 00:39:36 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 90.1 seconds
RetCode: 0
Status:  OK 
CheckDir: CSSP.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/CSSP.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.1.2’
* 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 ... [4s/5s] 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘methods’ ‘stats’ ‘utils’
  All declared Imports should be used.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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 ... [45s/47s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
cssp.power-methods 32.447  0.565  33.778
cssp.fit-methods    9.461  0.119   9.852
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘run_tests.R’ [6s/6s]
 [6s/7s] 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/CSSP.Rcheck/00check.log’
for details.

CSSP.Rcheck/00install.out:

* installing *source* package ‘CSSP’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c bincount.c -o bincount.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c binpower.c -o binpower.o
binpower.c: In function ‘binpower’:
binpower.c:72: warning: suggest parentheses around comparison in operand of &
binpower.c:105: warning: suggest parentheses around comparison in operand of &
binpower.c: In function ‘binpower_pval’:
binpower.c:162: warning: suggest parentheses around comparison in operand of &
binpower.c:141: warning: unused variable ‘tmp’
binpower.c:141: warning: unused variable ‘sim_bin’
binpower.c:136: warning: unused variable ‘rscale_back’
binpower.c:136: warning: unused variable ‘rsize_back’
binpower.c:135: warning: unused variable ‘k’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c gridLogMean.c -o gridLogMean.o
gridLogMean.c: In function ‘gridMGClogmean_c’:
gridLogMean.c:29: warning: suggest parentheses around comparison in operand of &
gridLogMean.c:29: warning: suggest parentheses around comparison in operand of |
gridLogMean.c:29: warning: suggest parentheses around comparison in operand of |
gridLogMean.c:29: warning: suggest parentheses around comparison in operand of &
gridLogMean.c:35: warning: suggest parentheses around comparison in operand of |
gridLogMean.c:35: warning: suggest parentheses around comparison in operand of &
gridLogMean.c:35: warning: suggest parentheses around comparison in operand of &
gridLogMean.c:35: warning: suggest parentheses around comparison in operand of &
gridLogMean.c:43: warning: suggest parentheses around comparison in operand of &
gridLogMean.c:45: warning: suggest parentheses around comparison in operand of |
gridLogMean.c:77: warning: suggest parentheses around comparison in operand of &
gridLogMean.c:77: warning: suggest parentheses around comparison in operand of &
gridLogMean.c:77: warning: suggest parentheses around comparison in operand of &
gridLogMean.c:157: warning: suggest parentheses around comparison in operand of &
gridLogMean.c:157: warning: suggest parentheses around comparison in operand of &
gridLogMean.c:157: warning: suggest parentheses around comparison in operand of &
gridLogMean.c:10: warning: unused variable ‘counter’
gridLogMean.c: In function ‘gridMlogmean_c’:
gridLogMean.c:193: warning: suggest parentheses around comparison in operand of |
gridLogMean.c:193: warning: suggest parentheses around comparison in operand of &
gridLogMean.c:199: warning: suggest parentheses around comparison in operand of &
gridLogMean.c:199: warning: suggest parentheses around comparison in operand of &
gridLogMean.c:225: warning: suggest parentheses around comparison in operand of &
gridLogMean.c:295: warning: suggest parentheses around comparison in operand of &
gridLogMean.c:177: warning: unused variable ‘counter’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c gridMGC.c -o gridMGC.o
gridMGC.c: In function ‘gridMGC_c’:
gridMGC.c:29: warning: suggest parentheses around comparison in operand of |
gridMGC.c:29: warning: suggest parentheses around comparison in operand of &
gridMGC.c:29: warning: suggest parentheses around comparison in operand of &
gridMGC.c:29: warning: suggest parentheses around comparison in operand of &
gridMGC.c:37: warning: suggest parentheses around comparison in operand of &
gridMGC.c:39: warning: suggest parentheses around comparison in operand of |
gridMGC.c:71: warning: suggest parentheses around comparison in operand of &
gridMGC.c:71: warning: suggest parentheses around comparison in operand of &
gridMGC.c:71: warning: suggest parentheses around comparison in operand of &
gridMGC.c: In function ‘gridM_c’:
gridMGC.c:177: warning: suggest parentheses around comparison in operand of &
gridMGC.c:177: warning: suggest parentheses around comparison in operand of &
gridMGC.c:203: warning: suggest parentheses around comparison in operand of &
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c gridMean.c -o gridMean.o
gridMean.c: In function ‘gridMGCmean_c’:
gridMean.c:29: warning: suggest parentheses around comparison in operand of &
gridMean.c:29: warning: suggest parentheses around comparison in operand of |
gridMean.c:29: warning: suggest parentheses around comparison in operand of |
gridMean.c:29: warning: suggest parentheses around comparison in operand of &
gridMean.c:35: warning: suggest parentheses around comparison in operand of |
gridMean.c:35: warning: suggest parentheses around comparison in operand of &
gridMean.c:35: warning: suggest parentheses around comparison in operand of &
gridMean.c:35: warning: suggest parentheses around comparison in operand of &
gridMean.c:43: warning: suggest parentheses around comparison in operand of &
gridMean.c:45: warning: suggest parentheses around comparison in operand of |
gridMean.c:77: warning: suggest parentheses around comparison in operand of &
gridMean.c:77: warning: suggest parentheses around comparison in operand of &
gridMean.c:77: warning: suggest parentheses around comparison in operand of &
gridMean.c:157: warning: suggest parentheses around comparison in operand of &
gridMean.c:157: warning: suggest parentheses around comparison in operand of &
gridMean.c:157: warning: suggest parentheses around comparison in operand of &
gridMean.c:10: warning: unused variable ‘counter’
gridMean.c: In function ‘gridMmean_c’:
gridMean.c:193: warning: suggest parentheses around comparison in operand of |
gridMean.c:193: warning: suggest parentheses around comparison in operand of &
gridMean.c:199: warning: suggest parentheses around comparison in operand of &
gridMean.c:199: warning: suggest parentheses around comparison in operand of &
gridMean.c:225: warning: suggest parentheses around comparison in operand of &
gridMean.c:295: warning: suggest parentheses around comparison in operand of &
gridMean.c:177: warning: unused variable ‘counter’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c gridMode.c -o gridMode.o
gridMode.c: In function ‘gridMGCmode_c’:
gridMode.c:31: warning: suggest parentheses around comparison in operand of &
gridMode.c:31: warning: suggest parentheses around comparison in operand of |
gridMode.c:31: warning: suggest parentheses around comparison in operand of |
gridMode.c:31: warning: suggest parentheses around comparison in operand of &
gridMode.c:37: warning: suggest parentheses around comparison in operand of |
gridMode.c:37: warning: suggest parentheses around comparison in operand of &
gridMode.c:37: warning: suggest parentheses around comparison in operand of &
gridMode.c:37: warning: suggest parentheses around comparison in operand of &
gridMode.c:45: warning: suggest parentheses around comparison in operand of &
gridMode.c:47: warning: suggest parentheses around comparison in operand of |
gridMode.c:79: warning: suggest parentheses around comparison in operand of &
gridMode.c:79: warning: suggest parentheses around comparison in operand of &
gridMode.c:79: warning: suggest parentheses around comparison in operand of &
gridMode.c:164: warning: suggest parentheses around comparison in operand of &
gridMode.c:164: warning: suggest parentheses around comparison in operand of &
gridMode.c:164: warning: suggest parentheses around comparison in operand of &
gridMode.c: In function ‘gridMmode_c’:
gridMode.c:219: warning: suggest parentheses around comparison in operand of |
gridMode.c:219: warning: suggest parentheses around comparison in operand of &
gridMode.c:225: warning: suggest parentheses around comparison in operand of &
gridMode.c:225: warning: suggest parentheses around comparison in operand of &
gridMode.c:251: warning: suggest parentheses around comparison in operand of &
gridMode.c:326: warning: suggest parentheses around comparison in operand of &
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c gridNonpa.c -o gridNonpa.o
gridNonpa.c: In function ‘gridMGCnonpa_c’:
gridNonpa.c:29: warning: suggest parentheses around comparison in operand of &
gridNonpa.c:29: warning: suggest parentheses around comparison in operand of |
gridNonpa.c:29: warning: suggest parentheses around comparison in operand of |
gridNonpa.c:29: warning: suggest parentheses around comparison in operand of &
gridNonpa.c:35: warning: suggest parentheses around comparison in operand of |
gridNonpa.c:35: warning: suggest parentheses around comparison in operand of &
gridNonpa.c:35: warning: suggest parentheses around comparison in operand of &
gridNonpa.c:35: warning: suggest parentheses around comparison in operand of &
gridNonpa.c:43: warning: suggest parentheses around comparison in operand of &
gridNonpa.c:45: warning: suggest parentheses around comparison in operand of |
gridNonpa.c:77: warning: suggest parentheses around comparison in operand of &
gridNonpa.c:77: warning: suggest parentheses around comparison in operand of &
gridNonpa.c:77: warning: suggest parentheses around comparison in operand of &
gridNonpa.c:161: warning: suggest parentheses around comparison in operand of &
gridNonpa.c:161: warning: suggest parentheses around comparison in operand of &
gridNonpa.c:161: warning: suggest parentheses around comparison in operand of &
gridNonpa.c:10: warning: unused variable ‘counter’
gridNonpa.c: In function ‘gridMnonpa_c’:
gridNonpa.c:209: warning: suggest parentheses around comparison in operand of |
gridNonpa.c:209: warning: suggest parentheses around comparison in operand of &
gridNonpa.c:215: warning: suggest parentheses around comparison in operand of &
gridNonpa.c:215: warning: suggest parentheses around comparison in operand of &
gridNonpa.c:241: warning: suggest parentheses around comparison in operand of &
gridNonpa.c:315: warning: suggest parentheses around comparison in operand of &
gridNonpa.c:193: warning: unused variable ‘counter’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c gridSample.c -o gridSample.o
gridSample.c: In function ‘gridMGCsample_c’:
gridSample.c:33: warning: suggest parentheses around comparison in operand of &
gridSample.c:33: warning: suggest parentheses around comparison in operand of |
gridSample.c:33: warning: suggest parentheses around comparison in operand of |
gridSample.c:33: warning: suggest parentheses around comparison in operand of &
gridSample.c:39: warning: suggest parentheses around comparison in operand of |
gridSample.c:39: warning: suggest parentheses around comparison in operand of &
gridSample.c:39: warning: suggest parentheses around comparison in operand of &
gridSample.c:39: warning: suggest parentheses around comparison in operand of &
gridSample.c:47: warning: suggest parentheses around comparison in operand of &
gridSample.c:49: warning: suggest parentheses around comparison in operand of |
gridSample.c:81: warning: suggest parentheses around comparison in operand of &
gridSample.c:81: warning: suggest parentheses around comparison in operand of &
gridSample.c:81: warning: suggest parentheses around comparison in operand of &
gridSample.c:166: warning: suggest parentheses around comparison in operand of &
gridSample.c:166: warning: suggest parentheses around comparison in operand of &
gridSample.c:166: warning: suggest parentheses around comparison in operand of &
gridSample.c: In function ‘gridMsample_c’:
gridSample.c:224: warning: suggest parentheses around comparison in operand of |
gridSample.c:224: warning: suggest parentheses around comparison in operand of &
gridSample.c:230: warning: suggest parentheses around comparison in operand of &
gridSample.c:230: warning: suggest parentheses around comparison in operand of &
gridSample.c:256: warning: suggest parentheses around comparison in operand of &
gridSample.c:331: warning: suggest parentheses around comparison in operand of &
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c tag2bin.c -o tag2bin.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.13-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-class0.0090.0010.016
bindcount0.1570.0100.313
bindcount.chr0.0360.0020.074
callpeak-methods0.0250.0020.049
createBinData0.3960.0310.622
cssp.fit-methods9.4610.1199.852
cssp.power-methods32.447 0.56533.778
cssp.sim-methods0.0330.0170.050
fit.freq-methods0.3940.0340.428
pBBT-methods0.0160.0050.022
peakcount0.1130.0070.122
peakcount.chr0.0230.0040.027
qBBT-methods0.0470.0030.051
readBinFile0.0260.0080.034
tag2bin0.0220.0080.030
tag2bin.chr0.0120.0040.015