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) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 11:56:29 -0400 (Wed, 16 Oct 2019).
| Package 202/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CALIB 1.50.0 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 | |
| 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 |
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### Running command:
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### /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.
CALIB.Rcheck/00install.out
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### Running command:
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### /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)
CALIB.Rcheck/CALIB-Ex.timings
| name | user | system | elapsed | |
| RG | 0.165 | 0.008 | 0.173 | |
| adjustP2 | 0.235 | 0.000 | 0.235 | |
| calibReadMe | 0.001 | 0.000 | 0.001 | |
| cbind | 0.002 | 0.000 | 0.003 | |
| dim | 0.003 | 0.000 | 0.003 | |
| dimnames | 0.002 | 0.000 | 0.002 | |
| estimateParameter | 4.567 | 0.004 | 4.571 | |
| getColClasses | 0.001 | 0.000 | 0.001 | |
| merge | 0.006 | 0.000 | 0.006 | |
| normalizeData | 0.718 | 0.000 | 0.719 | |
| normdata | 0.111 | 0.004 | 0.114 | |
| parameter | 0.059 | 0.000 | 0.060 | |
| plotNormalizedData | 0.149 | 0.012 | 0.160 | |
| plotSpikeCI | 0.230 | 0.004 | 0.235 | |
| plotSpikeHI | 0.121 | 0.004 | 0.125 | |
| plotSpikeRG | 0.337 | 0.012 | 0.349 | |
| plotSpikeSpotError | 0.115 | 0.000 | 0.115 | |
| read.rg | 0 | 0 | 0 | |
| spike | 0.065 | 0.000 | 0.065 | |
| subsetting | 0.000 | 0.002 | 0.003 | |