Package: CALIB

Version: 1.44.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings CALIB_1.44.0.tar.gz

StartedAt: 2018-04-11 21:58:27 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 21:59:15 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 48.1 seconds

RetCode: 0

Status:  OK

CheckDir: CALIB.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings CALIB_1.44.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/CALIB.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-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 ‘1.44.0’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    arraydata   2.2Mb
    libs        2.7Mb
* 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 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
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’
Undefined global functions or variables:
  files namesInFun otherindex readBlueFuseHeader
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
estimateParameter 6.956      0   6.956
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/CALIB.Rcheck/00check.log’
for details.

* installing *source* package ‘CALIB’ ...
** libs
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c Design.cpp -o Design.o
g++  -I/home/biocbuild/bbs-3.6-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:147:78: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
  char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
                                                                              ^
Estimation.cpp:147:78: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Estimation.cpp:147:78: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Estimation.cpp:147:78: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Estimation.cpp:147:78: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Estimation.cpp:147:78: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Estimation.cpp:147:78: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Estimation.cpp:147:78: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c NormalizedData.cpp -o NormalizedData.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c ParameterofOneArray.cpp -o ParameterofOneArray.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c RawDataofOneArray.cpp -o RawDataofOneArray.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c SpikeofOneArray.cpp -o SpikeofOneArray.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o CALIB.so Design.o Estimation.o NormalizedData.o ParameterofOneArray.o RawDataofOneArray.o SpikeofOneArray.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-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)

name	user	system	elapsed
RG	0.140	0.012	0.155
adjustP2	0.260	0.004	0.265
calibReadMe	0.004	0.000	0.001
cbind	0.004	0.000	0.003
dim	0.004	0.000	0.003
dimnames	0.000	0.000	0.001
estimateParameter	6.956	0.000	6.956
getColClasses	0.000	0.000	0.001
merge	0.048	0.008	0.053
normalizeData	0.428	0.000	0.430
normdata	0.080	0.000	0.082
parameter	0.036	0.000	0.036
plotNormalizedData	0.132	0.004	0.133
plotSpikeCI	0.196	0.000	0.198
plotSpikeHI	0.080	0.000	0.077
plotSpikeRG	0.400	0.008	0.407
plotSpikeSpotError	0.088	0.000	0.087
read.rg	0.000	0.000	0.001
spike	0.036	0.000	0.036
subsetting	0.032	0.000	0.033