Gabriela Merino
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/TarSeqQC |
| Branch: RELEASE_3_7 |
| Last Commit: 657e2d3 |
| Last Changed Date: 2018-04-30 10:35:38 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:41:08 -0400 (Wed, 17 Oct 2018).
| Package 1465/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TarSeqQC 1.10.0 Gabriela Merino
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: TarSeqQC |
| Version: 1.10.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TarSeqQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings TarSeqQC_1.10.0.tar.gz |
| StartedAt: 2018-10-17 05:09:26 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 05:38:40 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 1754.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TarSeqQC.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TarSeqQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings TarSeqQC_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/TarSeqQC.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TarSeqQC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TarSeqQC' version '1.10.0'
* 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 'TarSeqQC' 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
* 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
plotNtdPercentage,TargetExperiment: no visible global function
definition for 'path'
plotRegion,TargetExperiment: no visible global function definition for
'path'
readFrequencies,TargetExperiment: no visible global function definition
for 'path'
Undefined global functions or variables:
path
* 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 ... NOTE
Error in .requirePackage(package) :
unable to find required package 'TarSeqQC'
Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
Execution halted
* 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
TargetExperiment-class 7.41 0.45 301.86
TargetExperiment-constructor 1.83 0.03 19.06
TargetExperiment-plotRegion 0.67 0.06 106.77
plotInOutFeatures 0.41 0.04 14.00
TargetExperiment-readFrequencies 0.32 0.03 14.57
TargetExperiment-plotFeature 0.27 0.03 68.56
TargetExperiment-plotNtdPercentage 0.14 0.00 27.00
pileupCounts 0.11 0.00 28.56
TargetExperiment-summarizePanel 0.04 0.05 15.38
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
TargetExperiment-class 9.14 0.31 370.65
TargetExperiment-constructor 1.95 0.17 16.57
TargetExperiment-plotRegion 0.62 0.07 95.70
TargetExperiment-readFrequencies 0.38 0.01 16.67
plotInOutFeatures 0.39 0.00 12.84
TargetExperiment-plotFeature 0.26 0.02 85.47
TargetExperiment-plotNtdPercentage 0.13 0.04 28.06
pileupCounts 0.14 0.03 24.64
TargetExperiment-summarizePanel 0.05 0.00 12.56
* 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-3.7-bioc/meat/TarSeqQC.Rcheck/00check.log'
for details.
TarSeqQC.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/TarSeqQC_1.10.0.tar.gz && rm -rf TarSeqQC.buildbin-libdir && mkdir TarSeqQC.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TarSeqQC.buildbin-libdir TarSeqQC_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL TarSeqQC_1.10.0.zip && rm TarSeqQC_1.10.0.tar.gz TarSeqQC_1.10.0.zip
###
##############################################################################
##############################################################################
% 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 1787k 100 1787k 0 0 22.7M 0 --:--:-- --:--:-- --:--:-- 24.9M
install for i386
* installing *source* package 'TarSeqQC' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'TarSeqQC'
finding HTML links ... done
TEList html
TarSeqQC-package html
TargetExperiment-biasExploration html
TargetExperiment-buildFeaturePanel html
TargetExperiment-buildReport html
TargetExperiment-class html
TargetExperiment-constructor html
TargetExperiment-getters html
TargetExperiment-initialize html
TargetExperiment-plot html
TargetExperiment-plotAttrExpl html
TargetExperiment-plotAttrPerform html
TargetExperiment-plotFeatPerform html
TargetExperiment-plotFeature html
TargetExperiment-plotGeneAttrPerFeat html
TargetExperiment-plotMetaDataExpl html
TargetExperiment-plotNtdPercentage html
TargetExperiment-plotRegion html
TargetExperiment-print html
TargetExperiment-readFrequencies html
TargetExperiment-setters html
TargetExperiment-show html
TargetExperiment-statistics html
TargetExperiment-summarizePanel html
TargetExperimentList-class html
TargetExperimentList-constructor html
TargetExperimentList-initialize html
TargetExperimentList-plotGlobalAttrExpl
html
TargetExperimentList-plotPoolPerformance
html
ampliPanel html
ampliPanel2 html
checkBedFasta html
myCounts html
object html
pileupCounts html
plotInOutFeatures html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'TarSeqQC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TarSeqQC' as TarSeqQC_1.10.0.zip
* DONE (TarSeqQC)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'TarSeqQC' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
TarSeqQC.Rcheck/tests_i386/runTests.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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("TarSeqQC")
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, colMeans, colSums, colnames,
dirname, 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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Attaching package: 'plyr'
The following object is masked from 'package:XVector':
compact
The following object is masked from 'package:IRanges':
desc
The following object is masked from 'package:S4Vectors':
rename
RUNIT TEST PROTOCOL -- Wed Oct 17 05:36:38 2018
***********************************************
Number of test functions: 33
Number of errors: 0
Number of failures: 0
1 Test Suite :
TarSeqQC RUnit Tests - 33 test functions, 0 errors, 0 failures
Number of test functions: 33
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
11.03 0.87 105.65
|
TarSeqQC.Rcheck/tests_x64/runTests.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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("TarSeqQC")
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, colMeans, colSums, colnames,
dirname, 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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Attaching package: 'plyr'
The following object is masked from 'package:XVector':
compact
The following object is masked from 'package:IRanges':
desc
The following object is masked from 'package:S4Vectors':
rename
RUNIT TEST PROTOCOL -- Wed Oct 17 05:38:33 2018
***********************************************
Number of test functions: 33
Number of errors: 0
Number of failures: 0
1 Test Suite :
TarSeqQC RUnit Tests - 33 test functions, 0 errors, 0 failures
Number of test functions: 33
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
11.93 0.59 114.64
|
|
TarSeqQC.Rcheck/examples_i386/TarSeqQC-Ex.timings
|
TarSeqQC.Rcheck/examples_x64/TarSeqQC-Ex.timings
|