| Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:06 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the GenomicFiles package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicFiles.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 743/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomicFiles 1.28.0 (landing page) Bioconductor Package Maintainer
| 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: GenomicFiles |
| Version: 1.28.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicFiles.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GenomicFiles_1.28.0.tar.gz |
| StartedAt: 2021-10-14 23:36:28 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 23:58:14 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 1306.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GenomicFiles.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:GenomicFiles.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GenomicFiles_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/GenomicFiles.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 'GenomicFiles/DESCRIPTION' ... OK
* this is package 'GenomicFiles' version '1.28.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'BiocGenerics', 'MatrixGenerics', 'GenomicRanges',
'SummarizedExperiment', 'BiocParallel', 'Rsamtools', 'rtracklayer'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'GenomicFiles' 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 ... OK
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
VcfStack-class 7.83 0.51 62.19
reduceByRange-methods 3.86 0.03 69.46
reduceByFile-methods 3.72 0.05 69.95
GenomicFiles-class 2.85 0.06 37.41
reduceByYield 1.52 0.06 22.37
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
VcfStack-class 8.57 0.25 61.07
reduceByRange-methods 4.69 0.04 71.67
reduceByFile-methods 4.47 0.05 75.19
GenomicFiles-class 3.15 0.04 38.20
reduceByYield 1.70 0.10 22.65
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'GenomicFiles_unit_tests.R'
OK
** running tests for arch 'x64' ...
Running 'GenomicFiles_unit_tests.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/GenomicFiles.Rcheck/00check.log'
for details.
GenomicFiles.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/GenomicFiles_1.28.0.tar.gz && rm -rf GenomicFiles.buildbin-libdir && mkdir GenomicFiles.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicFiles.buildbin-libdir GenomicFiles_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL GenomicFiles_1.28.0.zip && rm GenomicFiles_1.28.0.tar.gz GenomicFiles_1.28.0.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 290k 100 290k 0 0 930k 0 --:--:-- --:--:-- --:--:-- 931k
install for i386
* installing *source* package 'GenomicFiles' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'GenomicFiles'
finding HTML links ... done
GenomicFiles-class html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/GenomicFiles.buildbin-libdir/00LOCK-GenomicFiles/00new/GenomicFiles/help/GenomicFiles+2CGenomicRanges_OR_GRangesList+2Clist-method.html
GenomicFiles-deprecated html
VcfStack-class html
pack-methods html
reduceByFile-methods html
reduceByRange-methods html
reduceByYield html
registry-utils html
unpack-methods html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/GenomicFiles.buildbin-libdir/00LOCK-GenomicFiles/00new/GenomicFiles/help/unpack+2CList+2CGRangesList-method.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 'GenomicFiles' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicFiles' as GenomicFiles_1.28.0.zip
* DONE (GenomicFiles)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'GenomicFiles' successfully unpacked and MD5 sums checked
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GenomicFiles.Rcheck/tests_i386/GenomicFiles_unit_tests.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("GenomicFiles")
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: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
RUNIT TEST PROTOCOL -- Thu Oct 14 23:54:13 2021
***********************************************
Number of test functions: 20
Number of errors: 0
Number of failures: 0
1 Test Suite :
GenomicFiles RUnit Tests - 20 test functions, 0 errors, 0 failures
Number of test functions: 20
Number of errors: 0
Number of failures: 0
Warning message:
In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 1 out-of-bound range located on sequence 19.
Note that ranges located on a sequence whose length is unknown (NA) or
on a circular sequence are not considered out-of-bound (use
seqlengths() and isCircular() to get the lengths and circularity flags
of the underlying sequences). You can use trim() to trim these ranges.
See ?`trim,GenomicRanges-method` for more information.
>
> proc.time()
user system elapsed
59.31 1.82 219.36
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GenomicFiles.Rcheck/tests_x64/GenomicFiles_unit_tests.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("GenomicFiles")
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: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
RUNIT TEST PROTOCOL -- Thu Oct 14 23:58:06 2021
***********************************************
Number of test functions: 20
Number of errors: 0
Number of failures: 0
1 Test Suite :
GenomicFiles RUnit Tests - 20 test functions, 0 errors, 0 failures
Number of test functions: 20
Number of errors: 0
Number of failures: 0
Warning message:
In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 1 out-of-bound range located on sequence 19.
Note that ranges located on a sequence whose length is unknown (NA) or
on a circular sequence are not considered out-of-bound (use
seqlengths() and isCircular() to get the lengths and circularity flags
of the underlying sequences). You can use trim() to trim these ranges.
See ?`trim,GenomicRanges-method` for more information.
>
> proc.time()
user system elapsed
65.17 0.79 232.32
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GenomicFiles.Rcheck/examples_i386/GenomicFiles-Ex.timings
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GenomicFiles.Rcheck/examples_x64/GenomicFiles-Ex.timings
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