| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:22:58 -0400 (Wed, 15 Apr 2020).
| Package 682/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GenomicFiles 1.22.0 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: GenomicFiles |
| Version: 1.22.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicFiles.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings GenomicFiles_1.22.0.tar.gz |
| StartedAt: 2020-04-15 03:26:51 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 03:50:26 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 1414.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GenomicFiles.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicFiles.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings GenomicFiles_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/GenomicFiles.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.22.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'BiocGenerics', '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 ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/GenomicFiles-class.Rd:111: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/VcfStack-class.Rd:78: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/VcfStack-class.Rd:98: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/VcfStack-class.Rd:129: file link 'VcfFileList' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/VcfStack-class.Rd:130: file link 'VcfFileList' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/VcfStack-class.Rd:133: file link 'seqinfo<-' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/VcfStack-class.Rd:139: file link 'seqlevelsStyle<-' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/VcfStack-class.Rd:143: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/VcfStack-class.Rd:148: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/VcfStack-class.Rd:155: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/VcfStack-class.Rd:162: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/VcfStack-class.Rd:170: file link 'genotypeToSnpMatrix' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/VcfStack-class.Rd:180: file link 'ScanVcfParam' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/VcfStack-class.Rd:227: file link 'VcfFile' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/VcfStack-class.Rd:227: file link 'VcfFileList' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/reduceByYield.Rd:12: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/reduceByYield.Rd:29: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/reduceByYield.Rd:121: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/reduceByYield.Rd:122: file link 'TabixFile' in package 'Rsamtools' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/GenomicFiles.Rcheck/00install.out' for details.
* 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 or elapsed time > 5s
user system elapsed
VcfStack-class 5.06 0.51 38.78
reduceByFile-methods 3.50 0.03 84.66
reduceByRange-methods 3.46 0.05 76.32
GenomicFiles-class 2.89 0.08 39.25
reduceByYield 1.29 0.06 31.32
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
VcfStack-class 7.19 0.19 42.53
reduceByRange-methods 4.57 0.04 80.05
reduceByFile-methods 4.41 0.07 88.13
GenomicFiles-class 4.23 0.03 42.95
reduceByYield 1.83 0.06 24.45
* 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 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/GenomicFiles.Rcheck/00check.log'
for details.
GenomicFiles.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/GenomicFiles_1.22.0.tar.gz && rm -rf GenomicFiles.buildbin-libdir && mkdir GenomicFiles.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicFiles.buildbin-libdir GenomicFiles_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL GenomicFiles_1.22.0.zip && rm GenomicFiles_1.22.0.tar.gz GenomicFiles_1.22.0.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
0 289k 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 289k 100 289k 0 0 685k 0 --:--:-- --:--:-- --:--:-- 691k
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
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/GenomicFiles-class.Rd:111: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
GenomicFiles-deprecated html
VcfStack-class html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/VcfStack-class.Rd:78: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/VcfStack-class.Rd:98: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/VcfStack-class.Rd:129: file link 'VcfFileList' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/VcfStack-class.Rd:130: file link 'VcfFileList' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/VcfStack-class.Rd:133: file link 'seqinfo<-' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/VcfStack-class.Rd:139: file link 'seqlevelsStyle<-' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/VcfStack-class.Rd:143: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/VcfStack-class.Rd:148: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/VcfStack-class.Rd:155: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/VcfStack-class.Rd:162: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/VcfStack-class.Rd:170: file link 'genotypeToSnpMatrix' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/VcfStack-class.Rd:180: file link 'ScanVcfParam' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/VcfStack-class.Rd:227: file link 'VcfFile' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/VcfStack-class.Rd:227: file link 'VcfFileList' in package 'VariantAnnotation' does not exist and so has been treated as a topic
pack-methods html
reduceByFile-methods html
reduceByRange-methods html
reduceByYield html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/reduceByYield.Rd:12: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/reduceByYield.Rd:29: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/reduceByYield.Rd:121: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYJxR1l/R.INSTALL26202dd777e8/GenomicFiles/man/reduceByYield.Rd:122: file link 'TabixFile' in package 'Rsamtools' does not exist and so has been treated as a topic
registry-utils html
unpack-methods 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_1.22.0.zip
* DONE (GenomicFiles)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'GenomicFiles' successfully unpacked and MD5 sums checked
|
GenomicFiles.Rcheck/tests_i386/GenomicFiles_unit_tests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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, 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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Warning messages:
1: In Ops.factor(left, right) : '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors
3: In Ops.factor(left, right) : '+' not meaningful for factors
4: Warning messages:
In Ops.factor(left, right) : '+' not meaningful for factors
1: In Ops.factor(left, right) : '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors
3: In Ops.factor(left, right) : '+' not meaningful for factors
4: In Ops.factor(left, right) : '+' not meaningful for factors
RUNIT TEST PROTOCOL -- Wed Apr 15 03:45:41 2020
***********************************************
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()
Warning messages:
1: In Ops.factor(left, right) : '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors
user system elapsed
Warning messages:
52.01 1.78 240.01
1: In Ops.factor(left, right) : '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors
Warning messages:
1: In Ops.factor(left, right) : '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors
|
GenomicFiles.Rcheck/tests_x64/GenomicFiles_unit_tests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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, 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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Warning messages:
1: In Ops.factor(left, right) : '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors
3: In Ops.factor(left, right) : '+' not meaningful for factors
4: In Ops.factor(left, right) : '+' not meaningful for factors
Warning messages:
1: In Ops.factor(left, right) : '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors
3: In Ops.factor(left, right) : '+' not meaningful for factors
4: In Ops.factor(left, right) : '+' not meaningful for factors
Warning messages:
1: Warning messages:
In Ops.factor(left, right) : '+' not meaningful for factors
2: 1: In Ops.factor(left, right) : '+' not meaningful for factors
In Ops.factor(left, right) : '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors
RUNIT TEST PROTOCOL -- Wed Apr 15 03:50:20 2020
***********************************************
Number of test functions: 20
Number of errors: 0
Number of failures: 0
1 Test Suite :
Warning messages:
1: In Ops.factor(left, right) : '+' not meaningful for factors
2: GenomicFiles RUnit TestsIn Ops.factor(left, right) : - '+' not meaningful for factors
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
69.90 0.78 278.86
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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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