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CHECK report for CALIB on malbec2

This page was generated on 2019-10-16 11:56:29 -0400 (Wed, 16 Oct 2019).

Package 202/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CALIB 1.50.0
Hui Zhao
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/CALIB
Branch: RELEASE_3_9
Last Commit: b958554
Last Changed Date: 2019-05-02 11:53:07 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: CALIB
Version: 1.50.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CALIB.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CALIB_1.50.0.tar.gz
StartedAt: 2019-10-16 00:14:46 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:15:31 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 45.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: CALIB.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CALIB.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CALIB_1.50.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/CALIB.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.50.0’
* 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 ... WARNING
Found the following significant warnings:
  Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/biocbuild/bbs-3.9-bioc/meat/CALIB.Rcheck/00install.out’ for details.
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  [.ParameterList [.RGList_CALIB [.SpikeList cbind.ParameterList
  cbind.RGList_CALIB cbind.SpikeList dim.RGList_CALIB dim.SpikeList
  dimnames.RGList_CALIB dimnames.SpikeList length.RGList_CALIB
  length.SpikeList merge.RGList_CALIB merge.SpikeList
  rbind.RGList_CALIB rbind.SpikeList
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... 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

Status: 1 WARNING, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/CALIB.Rcheck/00check.log’
for details.



Installation output

CALIB.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL CALIB
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘CALIB’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c Design.cpp -o Design.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-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: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
                                                                              ^
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
Estimation.cpp:147:78: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c NormalizedData.cpp -o NormalizedData.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c ParameterofOneArray.cpp -o ParameterofOneArray.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c RawDataofOneArray.cpp -o RawDataofOneArray.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c SpikeofOneArray.cpp -o SpikeofOneArray.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-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-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-CALIB/00new/CALIB/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CALIB)

Tests output


Example timings

CALIB.Rcheck/CALIB-Ex.timings

nameusersystemelapsed
RG0.1650.0080.173
adjustP20.2350.0000.235
calibReadMe0.0010.0000.001
cbind0.0020.0000.003
dim0.0030.0000.003
dimnames0.0020.0000.002
estimateParameter4.5670.0044.571
getColClasses0.0010.0000.001
merge0.0060.0000.006
normalizeData0.7180.0000.719
normdata0.1110.0040.114
parameter0.0590.0000.060
plotNormalizedData0.1490.0120.160
plotSpikeCI0.2300.0040.235
plotSpikeHI0.1210.0040.125
plotSpikeRG0.3370.0120.349
plotSpikeSpotError0.1150.0000.115
read.rg000
spike0.0650.0000.065
subsetting0.0000.0020.003