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BioC 2.13: CHECK report for CALIB on zin1

This page was generated on 2014-04-05 09:47:26 -0700 (Sat, 05 Apr 2014).

Package 107/750HostnameOS / ArchBUILDCHECKBUILD BIN
CALIB 1.28.0
Hui Zhao
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/CALIB
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
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: CALIB
Version: 1.28.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings CALIB_1.28.0.tar.gz
StartedAt: 2014-04-05 00:01:02 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 00:01:58 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 55.5 seconds
RetCode: 0
Status:  OK 
CheckDir: CALIB.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/CALIB.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CALIB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CALIB’ version ‘1.28.0’
* 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 ‘CALIB’ can be installed ... [14s/14s] OK
* checking installed package size ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    arraydata   2.2Mb
    libs        2.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘limma’ ‘methods’
A package should be listed in only one of these fields.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
read.rg: warning in scan(fullname, what = "", sep = sep, quote = quote,
  skip = 1, nlines = 1, quiet = TRUE, allowEscape = FALSE): partial
  argument match of 'allowEscape' to 'allowEscapes'
getColClasses: no visible global function definition for ‘namesInFun’
plotSpikeCI: no visible binding for global variable ‘otherindex’
read.rg: no visible global function definition for ‘readBlueFuseHeader’
read.spike: no visible binding for global variable ‘files’
* 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 installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘quickstart.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [11s/11s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
estimateParameter 7.172      0   7.185
* 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 were 4 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/CALIB.Rcheck/00check.log’
for details.

CALIB.Rcheck/00install.out:

* installing *source* package ‘CALIB’ ...
** libs
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Design.cpp -o Design.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Estimation.cpp -o Estimation.o
Estimation.cpp: In function ‘SEXPREC* estimation(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
Estimation.cpp:144:78: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Estimation.cpp:144:78: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Estimation.cpp:144:78: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Estimation.cpp:144:78: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Estimation.cpp:144:78: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Estimation.cpp:144:78: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Estimation.cpp:144:78: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Estimation.cpp:144:78: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c NormalizedData.cpp -o NormalizedData.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c ParameterofOneArray.cpp -o ParameterofOneArray.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c RawDataofOneArray.cpp -o RawDataofOneArray.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c SpikeofOneArray.cpp -o SpikeofOneArray.o
g++ -shared -L/usr/local/lib -o CALIB.so Design.o Estimation.o NormalizedData.o ParameterofOneArray.o RawDataofOneArray.o SpikeofOneArray.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/CALIB.Rcheck/CALIB/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 (CALIB)

CALIB.Rcheck/CALIB-Ex.timings:

nameusersystemelapsed
RG0.1720.0000.172
adjustP20.3880.0040.393
calibReadMe0.0040.0040.009
cbind0.020.000.02
dim0.0160.0080.023
dimnames0.0440.0000.042
estimateParameter7.1720.0007.185
getColClasses0.0080.0000.009
merge0.020.000.02
normalizeData0.7440.0040.751
normdata0.0960.0000.096
parameter0.0440.0000.044
plotNormalizedData0.120.000.12
plotSpikeCI0.1360.0000.136
plotSpikeHI0.1240.0040.126
plotSpikeRG0.3040.0000.306
plotSpikeSpotError0.0920.0000.090
read.rg0.0040.0000.005
spike0.0560.0000.056
subsetting0.0120.0000.012