VJ Carey
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/GGBase |
| Branch: RELEASE_3_7 |
| Last Commit: f1312ed |
| Last Changed Date: 2018-04-30 10:35:08 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:33:49 -0400 (Wed, 17 Oct 2018).
| Package 612/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GGBase 3.42.0 VJ Carey
| 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: GGBase |
| Version: 3.42.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GGBase.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings GGBase_3.42.0.tar.gz |
| StartedAt: 2018-10-17 02:19:42 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 02:28:24 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 521.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GGBase.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:GGBase.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings GGBase_3.42.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/GGBase.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 'GGBase/DESCRIPTION' ... OK
* this is package 'GGBase' version '3.42.0'
* 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 'GGBase' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp42YHZM/R.INSTALL13fc6369561b/GGBase/man/MAFfilter.Rd:37: file link 'col.summary' in package 'snpStats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp42YHZM/R.INSTALL13fc6369561b/GGBase/man/clipPCs.Rd:27: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp42YHZM/R.INSTALL13fc6369561b/GGBase/man/clipPCs.Rd:31: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp42YHZM/R.INSTALL13fc6369561b/GGBase/man/make_smlSet.Rd:22: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp42YHZM/R.INSTALL13fc6369561b/GGBase/man/smlSet-class.Rd:35: file link 'AssayData-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp42YHZM/R.INSTALL13fc6369561b/GGBase/man/smlSet-class.Rd:37: file link 'AnnotatedDataFrame-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp42YHZM/R.INSTALL13fc6369561b/GGBase/man/smlSet-class.Rd:41: file link 'MIAxE-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp42YHZM/R.INSTALL13fc6369561b/GGBase/man/smlSet-class.Rd:44: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp42YHZM/R.INSTALL13fc6369561b/GGBase/man/smlSet-class.Rd:65: file link 'nsFilter,ExpressionSet-method' in package 'genefilter' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/GGBase.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
getSS: no visible global function definition for 'installed.packages'
Undefined global functions or variables:
installed.packages
Consider adding
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
MAFfilter 6.78 0.48 36.67
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
MAFfilter 4.41 0.5 31.26
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'MAFfilter.R'
Running 'make.R'
Running 'plot_EvG.R'
OK
** running tests for arch 'x64' ...
Running 'MAFfilter.R'
Running 'make.R'
Running 'plot_EvG.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, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/GGBase.Rcheck/00check.log'
for details.
GGBase.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/GGBase_3.42.0.tar.gz && rm -rf GGBase.buildbin-libdir && mkdir GGBase.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GGBase.buildbin-libdir GGBase_3.42.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL GGBase_3.42.0.zip && rm GGBase_3.42.0.tar.gz GGBase_3.42.0.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 217k 100 217k 0 0 2707k 0 --:--:-- --:--:-- --:--:-- 3016k
install for i386
* installing *source* package 'GGBase' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'GGBase'
finding HTML links ... done
MAFfilter html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp42YHZM/R.INSTALL13fc6369561b/GGBase/man/MAFfilter.Rd:37: file link 'col.summary' in package 'snpStats' does not exist and so has been treated as a topic
clipPCs html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp42YHZM/R.INSTALL13fc6369561b/GGBase/man/clipPCs.Rd:27: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp42YHZM/R.INSTALL13fc6369561b/GGBase/man/clipPCs.Rd:31: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
externalize html
make_smlSet html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp42YHZM/R.INSTALL13fc6369561b/GGBase/man/make_smlSet.Rd:22: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
plot_EvG html
rsid-class html
finding level-2 HTML links ... done
smlSet-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp42YHZM/R.INSTALL13fc6369561b/GGBase/man/smlSet-class.Rd:35: file link 'AssayData-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp42YHZM/R.INSTALL13fc6369561b/GGBase/man/smlSet-class.Rd:37: file link 'AnnotatedDataFrame-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp42YHZM/R.INSTALL13fc6369561b/GGBase/man/smlSet-class.Rd:41: file link 'MIAxE-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp42YHZM/R.INSTALL13fc6369561b/GGBase/man/smlSet-class.Rd:44: file link 'eSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp42YHZM/R.INSTALL13fc6369561b/GGBase/man/smlSet-class.Rd:65: file link 'nsFilter,ExpressionSet-method' in package 'genefilter' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'GGBase' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GGBase' as GGBase_3.42.0.zip
* DONE (GGBase)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'GGBase' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
GGBase.Rcheck/tests_i386/MAFfilter.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.
> library(GGBase)
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
> if ("GGtools" %in% installed.packages()[,1]) {
+ s20 = getSS("GGtools", "20")
+ nsnp = ncol(smList(s20)[[1]])
+ s20f = MAFfilter(s20, lower=.1)
+ nsnp2 = ncol(smList(s20f)[[1]])
+ ( nsnp == 119921 & nsnp2 == 46755 )
+ }
[1] FALSE
>
> proc.time()
user system elapsed
11.39 1.31 67.43
|
GGBase.Rcheck/tests_x64/MAFfilter.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.
> library(GGBase)
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
> if ("GGtools" %in% installed.packages()[,1]) {
+ s20 = getSS("GGtools", "20")
+ nsnp = ncol(smList(s20)[[1]])
+ s20f = MAFfilter(s20, lower=.1)
+ nsnp2 = ncol(smList(s20f)[[1]])
+ ( nsnp == 119921 & nsnp2 == 46755 )
+ }
[1] FALSE
>
> proc.time()
user system elapsed
9.28 0.68 9.95
|
|
GGBase.Rcheck/tests_i386/make.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.
> library(GGBase)
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
> if ("GGtools" %in% installed.packages()[,1]) {
+ s20 = getSS("GGtools", "20")
+ remk = make_smlSet( as(s20, "ExpressionSet"), smList(s20) )
+ validObject(s20) & validObject(remk)
+ }
[1] TRUE
>
> proc.time()
user system elapsed
10.85 0.98 11.81
|
GGBase.Rcheck/tests_x64/make.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.
> library(GGBase)
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
> if ("GGtools" %in% installed.packages()[,1]) {
+ s20 = getSS("GGtools", "20")
+ remk = make_smlSet( as(s20, "ExpressionSet"), smList(s20) )
+ validObject(s20) & validObject(remk)
+ }
[1] TRUE
>
> proc.time()
user system elapsed
12.20 0.92 13.12
|
|
GGBase.Rcheck/tests_i386/plot_EvG.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.
> library(GGBase)
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
> if ("GGtools" %in% installed.packages()[,1]) {
+ s20 = getSS("GGtools", "20")
+ plot_EvG(genesym("CPNE1"), rsid("rs6060535"), s20)
+ }
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:Matrix':
colMeans, colSums, rowMeans, rowSums, which
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'S4Vectors'
The following object is masked from 'package:Matrix':
expand
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
>
> proc.time()
user system elapsed
11.51 0.92 12.43
|
GGBase.Rcheck/tests_x64/plot_EvG.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.
> library(GGBase)
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
> if ("GGtools" %in% installed.packages()[,1]) {
+ s20 = getSS("GGtools", "20")
+ plot_EvG(genesym("CPNE1"), rsid("rs6060535"), s20)
+ }
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:Matrix':
colMeans, colSums, rowMeans, rowSums, which
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'S4Vectors'
The following object is masked from 'package:Matrix':
expand
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
>
> proc.time()
user system elapsed
10.57 0.62 11.17
|
|
GGBase.Rcheck/examples_i386/GGBase-Ex.timings
|
GGBase.Rcheck/examples_x64/GGBase-Ex.timings
|