| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:38:33 -0400 (Wed, 17 Oct 2018).
| Package 595/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GenomicFiles 1.16.0 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK |  | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: GenomicFiles |
| Version: 1.16.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicFiles.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings GenomicFiles_1.16.0.tar.gz |
| StartedAt: 2018-10-17 02:15:28 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 02:39:02 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 1413.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GenomicFiles.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicFiles.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings GenomicFiles_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/GenomicFiles.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 'GenomicFiles/DESCRIPTION' ... OK
* this is package 'GenomicFiles' version '1.16.0'
* 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-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/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-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/GenomicFiles/man/VcfStack-class.Rd:77: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/GenomicFiles/man/VcfStack-class.Rd:97: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/GenomicFiles/man/VcfStack-class.Rd:128: file link 'VcfFileList' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/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-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/GenomicFiles/man/VcfStack-class.Rd:132: file link 'seqinfo<-' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/GenomicFiles/man/VcfStack-class.Rd:138: file link 'seqlevelsStyle<-' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/GenomicFiles/man/VcfStack-class.Rd:142: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/GenomicFiles/man/VcfStack-class.Rd:147: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/GenomicFiles/man/VcfStack-class.Rd:154: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/GenomicFiles/man/VcfStack-class.Rd:162: file link 'genotypeToSnpMatrix' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/GenomicFiles/man/VcfStack-class.Rd:172: file link 'ScanVcfParam' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/GenomicFiles/man/VcfStack-class.Rd:219: file link 'VcfFile' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/GenomicFiles/man/VcfStack-class.Rd:219: file link 'VcfFileList' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/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-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/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-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/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-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/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-3.7-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 4.25 0.78 56.40
reduceByYield 0.73 0.12 50.27
GenomicFiles-class 0.48 0.27 36.36
reduceByRange-methods 0.26 0.02 95.47
reduceByFile-methods 0.24 0.03 154.26
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
VcfStack-class 3.95 0.05 32.82
reduceByRange-methods 1.33 0.10 64.81
reduceByYield 0.70 0.03 23.41
GenomicFiles-class 0.53 0.06 30.55
reduceByFile-methods 0.20 0.03 68.39
* 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-3.7-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://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/GenomicFiles_1.16.0.tar.gz && rm -rf GenomicFiles.buildbin-libdir && mkdir GenomicFiles.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicFiles.buildbin-libdir GenomicFiles_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL GenomicFiles_1.16.0.zip && rm GenomicFiles_1.16.0.tar.gz GenomicFiles_1.16.0.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 4628k 0 --:--:-- --:--:-- --:--:-- 5278k
install for i386
* installing *source* package 'GenomicFiles' ...
** 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-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/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-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/GenomicFiles/man/VcfStack-class.Rd:77: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/GenomicFiles/man/VcfStack-class.Rd:97: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/GenomicFiles/man/VcfStack-class.Rd:128: file link 'VcfFileList' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/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-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/GenomicFiles/man/VcfStack-class.Rd:132: file link 'seqinfo<-' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/GenomicFiles/man/VcfStack-class.Rd:138: file link 'seqlevelsStyle<-' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/GenomicFiles/man/VcfStack-class.Rd:142: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/GenomicFiles/man/VcfStack-class.Rd:147: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/GenomicFiles/man/VcfStack-class.Rd:154: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/GenomicFiles/man/VcfStack-class.Rd:162: file link 'genotypeToSnpMatrix' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/GenomicFiles/man/VcfStack-class.Rd:172: file link 'ScanVcfParam' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/GenomicFiles/man/VcfStack-class.Rd:219: file link 'VcfFile' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/GenomicFiles/man/VcfStack-class.Rd:219: 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-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/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-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/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-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/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-3.7-bioc/tmpdir/Rtmpy6io1X/R.INSTALL20045a3d64de/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
In R CMD INSTALL
install for x64
* installing *source* package 'GenomicFiles' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicFiles' as GenomicFiles_1.16.0.zip
* DONE (GenomicFiles)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'GenomicFiles' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
GenomicFiles.Rcheck/tests_i386/GenomicFiles_unit_tests.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("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, 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
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
Attaching package: 'Biostrings'
The following object is masked from 'package:DelayedArray':
type
The following object is masked from 'package:base':
strsplit
Warning messages:
1: In Ops.factor(left, right) : '+' not meaningful for factors
2: Warning messages:
In Ops.factor(left, right) : '+' not meaningful for factors
1: 3: In Ops.factor(left, right) : '+' not meaningful for factors
In Ops.factor(left, right) :2: '+' not meaningful for factors
4: In Ops.factor(left, right) : '+' not meaningful for factors
3: In Ops.factor(left, right) : '+' not meaningful for factors
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
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 Oct 17 02:35:24 2018
***********************************************
Number of test functions: 19
Number of errors: 0
Number of failures: 0
1 Test Suite :
GenomicFiles RUnit Tests - 19 test functions, 0 errors, 0 failures
Number of test functions: 19
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
39.20 2.03 212.14
|
GenomicFiles.Rcheck/tests_x64/GenomicFiles_unit_tests.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("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, 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
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
Attaching package: 'Biostrings'
The following object is masked from 'package:DelayedArray':
type
The following object is masked from 'package:base':
strsplit
Warning messages:
Warning messages:
1: 1: In Ops.factor(left, right) : '+' not meaningful for factors
In Ops.factor(left, right) : '+' not meaningful for factors
2: 2: In Ops.factor(left, right) : '+' not meaningful for factors
In Ops.factor(left, right) :3: '+' not meaningful for factors
3: In Ops.factor(left, right) : '+' not meaningful for factors
4: In Ops.factor(left, right) : '+' not meaningful for factors
4: In Ops.factor(left, right) : '+' not meaningful for factors
In Ops.factor(left, right) : '+' not meaningful for factors
Warning messages:
Warning messages:
1: 1: In Ops.factor(left, right) : '+' not meaningful for factors
In Ops.factor(left, right) :2: '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors
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
RUNIT TEST PROTOCOL -- Wed Oct 17 02:38:54 2018
***********************************************
Number of test functions: 19
Number of errors: 0
Number of failures: 0
1 Test Suite :
GenomicFiles RUnit Tests - 19 test functions, 0 errors, 0 failures
Number of test functions: 19
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
35.64 0.90 209.76
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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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