Cuilan lani Gao
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/AGDEX |
| Branch: RELEASE_3_10 |
| Last Commit: f34d12b |
| Last Changed Date: 2019-10-29 13:08:22 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:20:12 -0400 (Wed, 15 Apr 2020).
| Package 37/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| AGDEX 1.34.0 Cuilan lani Gao
| 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: AGDEX |
| Version: 1.34.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AGDEX.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings AGDEX_1.34.0.tar.gz |
| StartedAt: 2020-04-15 01:12:18 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 01:14:31 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 133.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: AGDEX.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AGDEX.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings AGDEX_1.34.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/AGDEX.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 'AGDEX/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AGDEX' version '1.34.0'
* 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 'AGDEX' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpWQq39k/R.INSTALLd342a66aea/AGDEX/man/agdex.Rd:91: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpWQq39k/R.INSTALLd342a66aea/AGDEX/man/agdex.Rd:93: file link 'GeneSetCollection' in package 'GSEABase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpWQq39k/R.INSTALLd342a66aea/AGDEX/man/gset.data.Rd:24: file link 'GeneSetCollection' in package 'GSEABase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpWQq39k/R.INSTALLd342a66aea/AGDEX/man/human.data.Rd:35: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpWQq39k/R.INSTALLd342a66aea/AGDEX/man/make.dex.set.object.Rd:37: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpWQq39k/R.INSTALLd342a66aea/AGDEX/man/make.dex.set.object.Rd:39: file link 'GeneSetCollection' in package 'GSEABase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpWQq39k/R.INSTALLd342a66aea/AGDEX/man/mouse.data.Rd:35: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/AGDEX.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.
Non-standard license specification:
GPL Version 2 or later
Standardizable: TRUE
Standardized license specification:
GPL (>= 2)
* 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
Packages in Depends field not imported from:
'Biobase' 'GSEABase'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
agdex: no visible global function definition for 'exprs'
agdex: no visible global function definition for 'qnorm'
agdex: no visible global function definition for 'pnorm'
agdex: no visible global function definition for 'sampleNames'
agdex: no visible global function definition for 'pData'
agdex.scatterplot: no visible global function definition for 'plot'
agdex.scatterplot: no visible global function definition for 'points'
agdex.scatterplot: no visible global function definition for 'lines'
agdex.scatterplot: no visible global function definition for 'prcomp'
agdex.scatterplot: no visible global function definition for 'abline'
gsc.to.index.list: no visible global function definition for 'geneIds'
prep.dex.set: no visible global function definition for 'exprs'
prep.dex.set: no visible global function definition for 'pData'
read.agdex.gset.details: no visible global function definition for
'read.table'
read.agdex.gset.list: no visible global function definition for
'read.table'
read.agdex.result: no visible global function definition for
'read.table'
read.enrich.gset.list: no visible global function definition for
'read.table'
read.gset.collection: no visible global function definition for
'read.table'
read.gset.collection: no visible global function definition for
'GeneSet'
read.gset.collection: no visible global function definition for
'geneIds<-'
read.gset.collection: no visible global function definition for
'GeneSetCollection'
write.agdex.gset.details: no visible global function definition for
'write.table'
write.agdex.result: no visible global function definition for
'write.table'
write.gset.list.result: no visible global function definition for
'write.table'
Undefined global functions or variables:
GeneSet GeneSetCollection abline exprs geneIds geneIds<- lines pData
plot pnorm points prcomp qnorm read.table sampleNames write.table
Consider adding
importFrom("graphics", "abline", "lines", "plot", "points")
importFrom("stats", "pnorm", "prcomp", "qnorm")
importFrom("utils", "read.table", "write.table")
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
** running examples for arch 'x64' ... 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, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/AGDEX.Rcheck/00check.log'
for details.
AGDEX.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/AGDEX_1.34.0.tar.gz && rm -rf AGDEX.buildbin-libdir && mkdir AGDEX.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AGDEX.buildbin-libdir AGDEX_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL AGDEX_1.34.0.zip && rm AGDEX_1.34.0.tar.gz AGDEX_1.34.0.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 330k 100 330k 0 0 7729k 0 --:--:-- --:--:-- --:--:-- 8471k
install for i386
* installing *source* package 'AGDEX' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'AGDEX'
finding HTML links ... done
AGDEX-package html
agdex html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpWQq39k/R.INSTALLd342a66aea/AGDEX/man/agdex.Rd:91: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpWQq39k/R.INSTALLd342a66aea/AGDEX/man/agdex.Rd:93: file link 'GeneSetCollection' in package 'GSEABase' does not exist and so has been treated as a topic
agdex.res html
agdex.scatterplot html
get.gset.result.details html
gset.data html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpWQq39k/R.INSTALLd342a66aea/AGDEX/man/gset.data.Rd:24: file link 'GeneSetCollection' in package 'GSEABase' does not exist and so has been treated as a topic
human.data html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpWQq39k/R.INSTALLd342a66aea/AGDEX/man/human.data.Rd:35: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
make.dex.set.object html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpWQq39k/R.INSTALLd342a66aea/AGDEX/man/make.dex.set.object.Rd:37: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpWQq39k/R.INSTALLd342a66aea/AGDEX/man/make.dex.set.object.Rd:39: file link 'GeneSetCollection' in package 'GSEABase' does not exist and so has been treated as a topic
map.data html
mouse.data html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpWQq39k/R.INSTALLd342a66aea/AGDEX/man/mouse.data.Rd:35: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
read.agdex.gset.details html
read.agdex.result html
write.agdex.gset.details html
write.agdex.result 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 'AGDEX' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AGDEX' as AGDEX_1.34.0.zip
* DONE (AGDEX)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'AGDEX' successfully unpacked and MD5 sums checked
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AGDEX.Rcheck/examples_i386/AGDEX-Ex.timings
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AGDEX.Rcheck/examples_x64/AGDEX-Ex.timings
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