Li Chen
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/ChIPComp |
| Branch: RELEASE_3_6 |
| Last Commit: 8e68cd1 |
| Last Changed Date: 2017-10-30 12:40:53 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:26:44 -0400 (Thu, 12 Apr 2018).
| Package 216/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ChIPComp 1.8.0 Li Chen
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: ChIPComp |
| Version: 1.8.0 |
| Command: rm -rf ChIPComp.buildbin-libdir ChIPComp.Rcheck && mkdir ChIPComp.buildbin-libdir ChIPComp.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPComp.buildbin-libdir ChIPComp_1.8.0.tar.gz >ChIPComp.Rcheck\00install.out 2>&1 && cp ChIPComp.Rcheck\00install.out ChIPComp-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ChIPComp.buildbin-libdir --install="check:ChIPComp-install.out" --force-multiarch --no-vignettes --timings ChIPComp_1.8.0.tar.gz |
| StartedAt: 2018-04-11 22:50:43 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 22:56:36 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 352.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ChIPComp.Rcheck |
| Warnings: 0 |
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### Running command:
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### rm -rf ChIPComp.buildbin-libdir ChIPComp.Rcheck && mkdir ChIPComp.buildbin-libdir ChIPComp.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPComp.buildbin-libdir ChIPComp_1.8.0.tar.gz >ChIPComp.Rcheck\00install.out 2>&1 && cp ChIPComp.Rcheck\00install.out ChIPComp-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ChIPComp.buildbin-libdir --install="check:ChIPComp-install.out" --force-multiarch --no-vignettes --timings ChIPComp_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ChIPComp.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChIPComp/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPComp' version '1.8.0'
* 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 whether package 'ChIPComp' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
ChIPComp: no visible global function definition for 'queryHits'
ChIPComp: no visible global function definition for 'pnorm'
findCommonPeak: no visible global function definition for 'ppois'
getCTCounts: no visible global function definition for 'seqlevels'
getCTCounts: no visible global function definition for 'seqnames'
getCTCounts: no visible global function definition for 'subjectHits'
getCTCounts: no visible global function definition for 'queryHits'
makeConf: no visible global function definition for 'read.csv'
makeConf: no visible global function definition for 'model.matrix'
makePeakSet: no visible global function definition for 'subjectHits'
plot.ChIPComp : mypar: no visible global function definition for 'par'
plot.ChIPComp: no visible global function definition for 'lm'
plot.ChIPComp: no visible global function definition for 'coef'
plot.ChIPComp: no visible global function definition for 'plot'
plot.ChIPComp: no visible global function definition for
'smooth.spline'
plot.ChIPComp: no visible global function definition for 'lines'
regress: no visible global function definition for 'lm'
regress: no visible global function definition for 'coef'
regress: no visible global function definition for 'resid'
regress: no visible global function definition for 'smooth.spline'
regress: no visible global function definition for 'predict'
rmdup: no visible global function definition for 'qbinom'
Undefined global functions or variables:
coef lines lm model.matrix par plot pnorm ppois predict qbinom
queryHits read.csv resid seqlevels seqnames smooth.spline subjectHits
Consider adding
importFrom("graphics", "lines", "par", "plot")
importFrom("stats", "coef", "lm", "model.matrix", "pnorm", "ppois",
"predict", "qbinom", "resid", "smooth.spline")
importFrom("utils", "read.csv")
to your NAMESPACE file.
* 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ChIPComp.buildbin-libdir/ChIPComp/libs/i386/ChIPComp.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
makeCountSet 17.33 1.22 18.55
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
makeCountSet 18.71 1.05 19.75
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.R'
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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/ChIPComp.Rcheck/00check.log'
for details.
ChIPComp.Rcheck/00install.out
install for i386
* installing *source* package 'ChIPComp' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c mva.c -o mva.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o ChIPComp.dll tmp.def mva.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/ChIPComp.buildbin-libdir/ChIPComp/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'ChIPComp'
finding HTML links ... done
ChIPComp-package html
ChIPComp html
makeConf html
makeCountSet html
plot html
print html
seqData html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'ChIPComp' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c mva.c -o mva.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o ChIPComp.dll tmp.def mva.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/ChIPComp.buildbin-libdir/ChIPComp/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChIPComp' as ChIPComp_1.8.0.zip
* DONE (ChIPComp)
In R CMD INSTALL
In R CMD INSTALL
|
ChIPComp.Rcheck/tests_i386/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("ChIPComp")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Making peak list......
Making ip counts......
Making control counts......
RUNIT TEST PROTOCOL -- Wed Apr 11 22:56:03 2018
***********************************************
Number of test functions: 3
Number of errors: 0
Number of failures: 0
1 Test Suite :
ChIPComp RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
19.70 1.35 21.04
|
ChIPComp.Rcheck/tests_x64/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("ChIPComp")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Making peak list......
Making ip counts......
Making control counts......
RUNIT TEST PROTOCOL -- Wed Apr 11 22:56:31 2018
***********************************************
Number of test functions: 3
Number of errors: 0
Number of failures: 0
1 Test Suite :
ChIPComp RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
26.20 1.14 27.32
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ChIPComp.Rcheck/examples_i386/ChIPComp-Ex.timings
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ChIPComp.Rcheck/examples_x64/ChIPComp-Ex.timings
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