Charles Joly Beauparlant
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/metagene |
| Branch: RELEASE_3_9 |
| Last Commit: 89b13a0 |
| Last Changed Date: 2019-05-02 11:53:48 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:30:44 -0400 (Wed, 16 Oct 2019).
| Package 961/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| metagene 2.16.0 Charles Joly Beauparlant
| 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 | OK | OK | |
| Package: metagene |
| Version: 2.16.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metagene.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings metagene_2.16.0.tar.gz |
| StartedAt: 2019-10-16 05:04:38 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:14:37 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 598.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: metagene.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:metagene.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings metagene_2.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/metagene.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 'metagene/DESCRIPTION' ... OK
* this is package 'metagene' version '2.16.0'
* 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 'metagene' can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.0Mb
sub-directories of 1Mb or more:
extdata 5.4Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
'similaRpeak'
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
* 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
avoid_gaps_update: no visible binding for global variable 'value'
avoid_gaps_update: no visible binding for global variable 'bam'
avoid_gaps_update: no visible binding for global variable 'tab'
avoid_gaps_update: no visible binding for global variable 'nuc'
permutation_test: no visible global function definition for '.'
permutation_test: no visible binding for global variable 'value'
plot_metagene: no visible binding for global variable 'bin'
plot_metagene: no visible binding for global variable 'value'
plot_metagene: no visible binding for global variable 'qinf'
plot_metagene: no visible binding for global variable 'qsup'
plot_metagene: no visible binding for global variable 'group'
plot_metagene: no visible binding for global variable 'nuc'
plot_metagene: no visible binding for global variable 'design'
plot_metagene: no visible binding for global variable 'nuctot'
Undefined global functions or variables:
. bam bin design group nuc nuctot qinf qsup tab value
* 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 R/sysdata.rda ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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/metagene.Rcheck/00check.log'
for details.
metagene.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/metagene_2.16.0.tar.gz && rm -rf metagene.buildbin-libdir && mkdir metagene.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=metagene.buildbin-libdir metagene_2.16.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL metagene_2.16.0.zip && rm metagene_2.16.0.tar.gz metagene_2.16.0.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
39 4870k 39 1936k 0 0 25.7M 0 --:--:-- --:--:-- --:--:-- 27.8M
100 4870k 100 4870k 0 0 48.1M 0 --:--:-- --:--:-- --:--:-- 50.6M
install for i386
* installing *source* package 'metagene' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'metagene'
finding HTML links ... done
Bam_Handler html
avoid_gaps_update html
bed_file_filter html
exon_by_gene_with_observed_transcripts
html
get_demo_bam_files html
get_demo_design html
get_demo_metagene html
get_demo_regions html
get_promoters_txdb html
metagene html
permutation_test html
plot_metagene html
promoters_hg18 html
promoters_hg19 html
promoters_mm10 html
promoters_mm9 html
write_bed_file_filter_result 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 'metagene' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'metagene' as metagene_2.16.0.zip
* DONE (metagene)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'metagene' successfully unpacked and MD5 sums checked
|
metagene.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.
> ## Run all tests in the metagene package
> BiocGenerics:::testPackage("metagene")
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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
ChIP-Seq flip/unflip
produce data table : ChIP-Seq
[1] TRUE
Normalization done
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
produce data table : ChIP-Seq
ChIP-Seq flip/unflip
ChIP-Seq flip/unflip
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
[1] TRUE
RUNIT TEST PROTOCOL -- Wed Oct 16 05:12:48 2019
***********************************************
Number of test functions: 205
Number of errors: 0
Number of failures: 0
1 Test Suite :
metagene RUnit Tests - 205 test functions, 0 errors, 0 failures
Number of test functions: 205
Number of errors: 0
Number of failures: 0
There were 50 or more warnings (use warnings() to see the first 50)
>
> proc.time()
user system elapsed
95.35 9.39 105.35
|
metagene.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.
> ## Run all tests in the metagene package
> BiocGenerics:::testPackage("metagene")
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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
ChIP-Seq flip/unflip
produce data table : ChIP-Seq
[1] TRUE
Normalization done
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
produce data table : ChIP-Seq
ChIP-Seq flip/unflip
ChIP-Seq flip/unflip
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
[1] TRUE
RUNIT TEST PROTOCOL -- Wed Oct 16 05:14:30 2019
***********************************************
Number of test functions: 205
Number of errors: 0
Number of failures: 0
1 Test Suite :
metagene RUnit Tests - 205 test functions, 0 errors, 0 failures
Number of test functions: 205
Number of errors: 0
Number of failures: 0
There were 50 or more warnings (use warnings() to see the first 50)
>
> proc.time()
user system elapsed
94.25 7.93 101.95
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metagene.Rcheck/examples_i386/metagene-Ex.timings
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metagene.Rcheck/examples_x64/metagene-Ex.timings
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