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This page was generated on 2021-10-15 15:06:19 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the riboSeqR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/riboSeqR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1582/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| riboSeqR 1.26.0 (landing page) Thomas J. Hardcastle
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: riboSeqR |
| Version: 1.26.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:riboSeqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings riboSeqR_1.26.0.tar.gz |
| StartedAt: 2021-10-15 04:35:17 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 04:38:09 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 172.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: riboSeqR.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:riboSeqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings riboSeqR_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/riboSeqR.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'riboSeqR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'riboSeqR' 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 ... OK
* checking for portable file names ... OK
* checking whether package 'riboSeqR' 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
.readAlignments : <anonymous>: no visible global function definition
for 'read.delim'
filterHits : <anonymous> : <anonymous>: no visible global function
definition for 'chisq.test'
frameCounting : getHits: no visible global function definition for
'queryHits'
frameCounting : getHits: no visible global function definition for
'subjectHits'
lengthDist: no visible global function definition for 'modifyList'
lengthDist: no visible global function definition for 'rainbow'
lengthDist: no visible binding for global variable 'lines'
plotCDS: no visible global function definition for 'dev.list'
plotCDS: no visible global function definition for 'par'
plotCDS : <anonymous> : <anonymous> : makeMatz: no visible binding for
global variable 'weighted.mean'
plotCDS : <anonymous> : <anonymous>: no visible global function
definition for 'barplot'
plotCDS : <anonymous> : <anonymous>: no visible global function
definition for 'rainbow'
plotCDS : <anonymous> : <anonymous>: no visible global function
definition for 'axis'
plotFS: no visible global function definition for 'barplot'
plotFS: no visible global function definition for 'rainbow'
plotTranscript: no visible global function definition for 'dev.list'
plotTranscript: no visible global function definition for 'par'
plotTranscript: no visible global function definition for 'barplot'
plotTranscript: no visible global function definition for 'axis'
plotTranscript: no visible global function definition for 'rect'
plotTranscript: no visible global function definition for 'text'
plotTranscript: no visible global function definition for 'rgb'
plotTranscript: no visible global function definition for 'segments'
rnaCounts : <anonymous>: no visible global function definition for
'subjectHits'
Undefined global functions or variables:
axis barplot chisq.test dev.list lines modifyList par queryHits
rainbow read.delim rect rgb segments subjectHits text weighted.mean
Consider adding
importFrom("grDevices", "dev.list", "rainbow", "rgb")
importFrom("graphics", "axis", "barplot", "lines", "par", "rect",
"segments", "text")
importFrom("stats", "chisq.test", "weighted.mean")
importFrom("utils", "modifyList", "read.delim")
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 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: 1 NOTE
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/riboSeqR.Rcheck/00check.log'
for details.
riboSeqR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/riboSeqR_1.26.0.tar.gz && rm -rf riboSeqR.buildbin-libdir && mkdir riboSeqR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=riboSeqR.buildbin-libdir riboSeqR_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL riboSeqR_1.26.0.zip && rm riboSeqR_1.26.0.tar.gz riboSeqR_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
26 3547k 26 924k 0 0 1468k 0 0:00:02 --:--:-- 0:00:02 1469k
100 3547k 100 3547k 0 0 2230k 0 0:00:01 0:00:01 --:--:-- 2231k
install for i386
* installing *source* package 'riboSeqR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'riboSeqR'
finding HTML links ... done
filterHits html
findCDS html
frameCounting html
frameShift html
lengthDist html
libScales html
logoContext html
plotCDS html
plotTranscript html
readRibodata html
riboCoding-class html
riboData-class html
riboSeqR-package html
rnaCounts html
sliceCounts 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 'riboSeqR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'riboSeqR' as riboSeqR_1.26.0.zip
* DONE (riboSeqR)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'riboSeqR' successfully unpacked and MD5 sums checked
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riboSeqR.Rcheck/tests_i386/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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("riboSeqR")
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.max, which.min
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
RUNIT TEST PROTOCOL -- Fri Oct 15 04:37:57 2021
***********************************************
Number of test functions: 0
Number of errors: 0
Number of failures: 0
1 Test Suite :
riboSeqR RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
4.17 0.45 4.59
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riboSeqR.Rcheck/tests_x64/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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("riboSeqR")
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.max, which.min
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
RUNIT TEST PROTOCOL -- Fri Oct 15 04:38:02 2021
***********************************************
Number of test functions: 0
Number of errors: 0
Number of failures: 0
1 Test Suite :
riboSeqR RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
4.70 0.18 4.87
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riboSeqR.Rcheck/examples_i386/riboSeqR-Ex.timings
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riboSeqR.Rcheck/examples_x64/riboSeqR-Ex.timings
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