Vanja Haberle
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/seqPattern |
| git_branch: RELEASE_3_13 |
| git_last_commit: 21a9de6 |
| git_last_commit_date: 2021-05-19 12:10:39 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:22 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the seqPattern package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/seqPattern.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 1739/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| seqPattern 1.24.0 (landing page) Vanja Haberle
| 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: seqPattern |
| Version: 1.24.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:seqPattern.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings seqPattern_1.24.0.tar.gz |
| StartedAt: 2021-10-15 05:31:49 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 05:35:13 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 203.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: seqPattern.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:seqPattern.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings seqPattern_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/seqPattern.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 'seqPattern/DESCRIPTION' ... OK
* this is package 'seqPattern' version '1.24.0'
* 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 'seqPattern' 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 ... NOTE
'library' or 'require' call to 'parallel' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.pattern.smoothscatter: no visible global function definition for
'mclapply'
.pattern.smoothscatter : <anonymous>: no visible global function
definition for 'png'
.pattern.smoothscatter : <anonymous>: no visible global function
definition for 'par'
.pattern.smoothscatter : <anonymous>: no visible global function
definition for 'colorRampPalette'
.pattern.smoothscatter : <anonymous>: no visible global function
definition for 'axis'
.pattern.smoothscatter : <anonymous>: no visible global function
definition for 'box'
.pattern.smoothscatter : <anonymous>: no visible global function
definition for 'lines'
.pattern.smoothscatter : <anonymous>: no visible global function
definition for 'text'
.pattern.smoothscatter : <anonymous>: no visible global function
definition for 'abline'
.pattern.smoothscatter : <anonymous>: no visible global function
definition for 'dev.off'
.pattern.smoothscatter: no visible global function definition for 'png'
.pattern.smoothscatter: no visible global function definition for 'par'
.pattern.smoothscatter: no visible global function definition for
'colorRampPalette'
.pattern.smoothscatter: no visible global function definition for
'axis'
.pattern.smoothscatter: no visible global function definition for 'box'
.pattern.smoothscatter: no visible global function definition for
'lines'
.pattern.smoothscatter: no visible global function definition for
'text'
.pattern.smoothscatter: no visible global function definition for
'abline'
.pattern.smoothscatter: no visible global function definition for
'dev.off'
.plot.motif.heatmap: no visible global function definition for 'par'
.plot.motif.heatmap: no visible global function definition for 'image'
.plot.motif.heatmap: no visible global function definition for 'axis'
.plot.motif.heatmap: no visible global function definition for 'box'
.plot.motif.heatmap: no visible global function definition for 'lines'
.plot.motif.heatmap: no visible global function definition for 'text'
.plot.motif.heatmap: no visible global function definition for 'abline'
.plot.windowed.average: no visible global function definition for
'rainbow'
.plot.windowed.average : <anonymous>: no visible global function
definition for 'lines'
.plot.windowed.average: no visible global function definition for
'legend'
.plot.windowed.average: no visible global function definition for
'abline'
.smoothScatter: no visible global function definition for
'colorRampPalette'
.smoothScatter: no visible binding for global variable 'blues9'
.smoothScatter: no visible binding for global variable 'box'
.smoothScatter: no visible global function definition for 'par'
.smoothScatter: no visible global function definition for 'xy.coords'
.smoothScatter: no visible global function definition for 'image'
.smoothScatter: no visible global function definition for 'points'
plotPatternOccurrenceAverage: no visible global function definition for
'rainbow'
getPatternOccurrenceList,DNAStringSet: no visible global function
definition for 'installed.packages'
getPatternOccurrenceList,DNAStringSet: no visible global function
definition for 'detectCores'
getPatternOccurrenceList,DNAStringSet: no visible global function
definition for 'mclapply'
plotMotifScanScores,DNAStringSet-matrix: no visible global function
definition for 'png'
plotMotifScanScores,DNAStringSet-matrix: no visible global function
definition for 'colorRampPalette'
plotMotifScanScores,DNAStringSet-matrix: no visible global function
definition for 'layout'
plotMotifScanScores,DNAStringSet-matrix: no visible global function
definition for 'par'
plotMotifScanScores,DNAStringSet-matrix: no visible global function
definition for 'box'
plotMotifScanScores,DNAStringSet-matrix: no visible global function
definition for 'dev.off'
plotPatternDensityMap,DNAStringSet: no visible global function
definition for 'installed.packages'
plotPatternDensityMap,DNAStringSet: no visible global function
definition for 'detectCores'
plotPatternOccurrenceAverage,DNAStringSet: no visible global function
definition for 'rainbow'
Undefined global functions or variables:
abline axis blues9 box colorRampPalette detectCores dev.off image
installed.packages layout legend lines mclapply par png points
rainbow text xy.coords
Consider adding
importFrom("grDevices", "blues9", "colorRampPalette", "dev.off", "png",
"rainbow", "xy.coords")
importFrom("graphics", "abline", "axis", "box", "image", "layout",
"legend", "lines", "par", "points", "text")
importFrom("utils", "installed.packages")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotPatternDensityMap 10.33 3.08 13.4
plotMotifDensityMap 6.46 0.85 7.3
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotPatternDensityMap 9.97 3.92 13.89
plotMotifDensityMap 7.00 1.08 8.08
* 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-3.13-bioc/meat/seqPattern.Rcheck/00check.log'
for details.
seqPattern.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/seqPattern_1.24.0.tar.gz && rm -rf seqPattern.buildbin-libdir && mkdir seqPattern.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=seqPattern.buildbin-libdir seqPattern_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL seqPattern_1.24.0.zip && rm seqPattern_1.24.0.tar.gz seqPattern_1.24.0.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
42 3306k 42 1415k 0 0 1239k 0 0:00:02 0:00:01 0:00:01 1239k
98 3306k 98 3272k 0 0 1673k 0 0:00:01 0:00:01 --:--:-- 1673k
100 3306k 100 3306k 0 0 1690k 0 0:00:01 0:00:01 --:--:-- 1690k
install for i386
* installing *source* package 'seqPattern' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'seqPattern'
finding HTML links ... done
TBPpwm html
getPatternOccurrenceList html
finding level-2 HTML links ... done
motifScanHits html
motifScanScores html
plotMotifDensityMap html
plotMotifOccurrenceAverage html
plotMotifScanScores html
plotPatternDensityMap html
plotPatternOccurrenceAverage html
seqPattern-package html
zebrafisPromoters html
zebrafisPromoters24h 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 'seqPattern' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'seqPattern' as seqPattern_1.24.0.zip
* DONE (seqPattern)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'seqPattern' successfully unpacked and MD5 sums checked
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seqPattern.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("seqPattern")
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.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
RUNIT TEST PROTOCOL -- Fri Oct 15 05:35:01 2021
***********************************************
Number of test functions: 6
Number of errors: 0
Number of failures: 0
1 Test Suite :
seqPattern RUnit Tests - 6 test functions, 0 errors, 0 failures
Number of test functions: 6
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
4.50 0.28 4.75
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seqPattern.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("seqPattern")
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.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
RUNIT TEST PROTOCOL -- Fri Oct 15 05:35:06 2021
***********************************************
Number of test functions: 6
Number of errors: 0
Number of failures: 0
1 Test Suite :
seqPattern RUnit Tests - 6 test functions, 0 errors, 0 failures
Number of test functions: 6
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
4.18 0.35 4.53
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seqPattern.Rcheck/examples_i386/seqPattern-Ex.timings
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seqPattern.Rcheck/examples_x64/seqPattern-Ex.timings
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