Jonathan Cairns
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/Rcade |
| Branch: RELEASE_3_9 |
| Last Commit: a918a8d |
| Last Changed Date: 2019-05-02 11:53:38 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:27:03 -0400 (Wed, 16 Oct 2019).
| Package 1322/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Rcade 1.26.0 Jonathan Cairns
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| 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: Rcade |
| Version: 1.26.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rcade.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Rcade_1.26.0.tar.gz |
| StartedAt: 2019-10-16 06:22:26 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:27:44 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 317.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Rcade.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rcade.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Rcade_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/Rcade.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rcade/DESCRIPTION' ... OK
* this is package 'Rcade' version '1.26.0'
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'Rcade' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.6Mb
sub-directories of 1Mb or more:
extdata 5.2Mb
* 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
* 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 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
constructRcadeTable: no visible binding for global variable 'p.DE'
constructRcadeTable: no visible binding for global variable 'p.ChIP'
plotBBB,Rcade: no visible global function definition for 'decorate3d'
Undefined global functions or variables:
decorate3d p.ChIP p.DE
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
RcadeAnalysis 5 0.32 6.97
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
RcadeAnalysis 6.39 0.14 6.55
* 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/Rcade.Rcheck/00check.log'
for details.
Rcade.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/Rcade_1.26.0.tar.gz && rm -rf Rcade.buildbin-libdir && mkdir Rcade.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rcade.buildbin-libdir Rcade_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL Rcade_1.26.0.zip && rm Rcade_1.26.0.tar.gz Rcade_1.26.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1604k 100 1604k 0 0 22.2M 0 --:--:-- --:--:-- --:--:-- 24.8M
install for i386
* installing *source* package 'Rcade' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Rcade'
finding HTML links ... done
Rcade-class html
RcadeAnalysis html
RcadeSTAT1 html
RcadeTrack-class html
constructRcadeTable html
countReads html
defineBins html
finding level-2 HTML links ... done
diffCountsBaySeq html
exportRcade-methods html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'Rcade' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rcade' as Rcade_1.26.0.zip
* DONE (Rcade)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'Rcade' successfully unpacked and MD5 sums checked
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Rcade.Rcheck/tests_i386/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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.
> require("Rcade") || stop("unable to load Rcade")
Loading required package: Rcade
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
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, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: baySeq
Loading required package: abind
Welcome to Rcade - version 1.26.0
If you are new to Rcade, please consider reading the vignette through the command: vignette("Rcade").
Attaching package: 'Rcade'
The following object is masked from 'package:BiocGenerics':
plotPCA
[1] TRUE
> BiocGenerics:::testPackage("Rcade")
File wgEncodeSydhTfbsHelas3InputIfng30StdAlnRep1.bam: Found 24 chromosomes, of which 0 are present in the annotation.
File wgEncodeSydhTfbsHelas3InputIfng30StdAlnRep1.bam: Removed all instances of 'chr' - now 19 chromosomes are present in the annotation.
File wgEncodeSydhTfbsHelas3InputStdAlnRep1.bam: Found 24 chromosomes, of which 0 are present in the annotation.
File wgEncodeSydhTfbsHelas3InputStdAlnRep1.bam: Removed all instances of 'chr' - now 19 chromosomes are present in the annotation.
File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep1.bam: Found 24 chromosomes, of which 0 are present in the annotation.
File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep1.bam: Removed all instances of 'chr' - now 19 chromosomes are present in the annotation.
File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep2.bam: Found 24 chromosomes, of which 0 are present in the annotation.
File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep2.bam: Removed all instances of 'chr' - now 19 chromosomes are present in the annotation.
File wgEncodeSydhTfbsHelas3InputIfng30StdAlnRep1.bam: Counting reads.
File wgEncodeSydhTfbsHelas3InputStdAlnRep1.bam: Counting reads.
File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep1.bam: Counting reads.
File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep2.bam: Counting reads.
RUNIT TEST PROTOCOL -- Wed Oct 16 06:27:21 2019
***********************************************
Number of test functions: 3
Number of errors: 0
Number of failures: 0
1 Test Suite :
Rcade 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
9.51 0.67 10.76
|
Rcade.Rcheck/tests_x64/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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.
> require("Rcade") || stop("unable to load Rcade")
Loading required package: Rcade
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
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, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: baySeq
Loading required package: abind
Welcome to Rcade - version 1.26.0
If you are new to Rcade, please consider reading the vignette through the command: vignette("Rcade").
Attaching package: 'Rcade'
The following object is masked from 'package:BiocGenerics':
plotPCA
[1] TRUE
> BiocGenerics:::testPackage("Rcade")
File wgEncodeSydhTfbsHelas3InputIfng30StdAlnRep1.bam: Found 24 chromosomes, of which 0 are present in the annotation.
File wgEncodeSydhTfbsHelas3InputIfng30StdAlnRep1.bam: Removed all instances of 'chr' - now 19 chromosomes are present in the annotation.
File wgEncodeSydhTfbsHelas3InputStdAlnRep1.bam: Found 24 chromosomes, of which 0 are present in the annotation.
File wgEncodeSydhTfbsHelas3InputStdAlnRep1.bam: Removed all instances of 'chr' - now 19 chromosomes are present in the annotation.
File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep1.bam: Found 24 chromosomes, of which 0 are present in the annotation.
File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep1.bam: Removed all instances of 'chr' - now 19 chromosomes are present in the annotation.
File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep2.bam: Found 24 chromosomes, of which 0 are present in the annotation.
File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep2.bam: Removed all instances of 'chr' - now 19 chromosomes are present in the annotation.
File wgEncodeSydhTfbsHelas3InputIfng30StdAlnRep1.bam: Counting reads.
File wgEncodeSydhTfbsHelas3InputStdAlnRep1.bam: Counting reads.
File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep1.bam: Counting reads.
File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep2.bam: Counting reads.
RUNIT TEST PROTOCOL -- Wed Oct 16 06:27:38 2019
***********************************************
Number of test functions: 3
Number of errors: 0
Number of failures: 0
1 Test Suite :
Rcade 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
15.81 0.50 16.29
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Rcade.Rcheck/examples_i386/Rcade-Ex.timings
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Rcade.Rcheck/examples_x64/Rcade-Ex.timings
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