Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 11:25:26 -0400 (Tue, 09 Apr 2019).
Package 199/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
CALIB 1.49.0 Hui Zhao
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
Package: CALIB |
Version: 1.49.0 |
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_1.49.0.tar.gz |
StartedAt: 2019-04-08 23:10:51 -0400 (Mon, 08 Apr 2019) |
EndedAt: 2019-04-08 23:11:33 -0400 (Mon, 08 Apr 2019) |
EllapsedTime: 42.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: CALIB.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### 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_1.49.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/CALIB.Rcheck’ * using R Under development (unstable) (2019-03-18 r76245) * 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 ‘1.49.0’ * 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 Examples with CPU or elapsed time > 5s user system elapsed estimateParameter 5.427 0.007 5.445 * 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.
CALIB.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL CALIB ### ############################################################################## ############################################################################## * 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)
CALIB.Rcheck/CALIB-Ex.timings
name | user | system | elapsed | |
RG | 0.165 | 0.008 | 0.173 | |
adjustP2 | 0.317 | 0.002 | 0.318 | |
calibReadMe | 0.001 | 0.000 | 0.001 | |
cbind | 0.003 | 0.000 | 0.003 | |
dim | 0.003 | 0.000 | 0.003 | |
dimnames | 0.000 | 0.001 | 0.001 | |
estimateParameter | 5.427 | 0.007 | 5.445 | |
getColClasses | 0.000 | 0.000 | 0.001 | |
merge | 0.005 | 0.003 | 0.007 | |
normalizeData | 0.696 | 0.004 | 0.700 | |
normdata | 0.109 | 0.004 | 0.114 | |
parameter | 0.058 | 0.000 | 0.059 | |
plotNormalizedData | 0.152 | 0.004 | 0.156 | |
plotSpikeCI | 0.241 | 0.004 | 0.244 | |
plotSpikeHI | 0.121 | 0.004 | 0.126 | |
plotSpikeRG | 0.337 | 0.004 | 0.340 | |
plotSpikeSpotError | 0.106 | 0.004 | 0.111 | |
read.rg | 0 | 0 | 0 | |
spike | 0.062 | 0.000 | 0.063 | |
subsetting | 0.003 | 0.000 | 0.003 | |