VJ Carey
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/erma |
| Branch: RELEASE_3_7 |
| Last Commit: 5d0e52f |
| Last Changed Date: 2018-04-30 10:35:37 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:40:44 -0400 (Wed, 17 Oct 2018).
| Package 461/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| erma 0.12.0 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: erma |
| Version: 0.12.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:erma.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings erma_0.12.0.tar.gz |
| StartedAt: 2018-10-17 01:51:51 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 02:00:34 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 522.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: erma.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:erma.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings erma_0.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/erma.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 'erma/DESCRIPTION' ... OK
* this is package 'erma' version '0.12.0'
* 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 'erma' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpay7ED9/R.INSTALL1a3c6847436/erma/man/genemodel.Rd:46: 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/Rtmpay7ED9/R.INSTALL1a3c6847436/erma/man/mapmeta.Rd:21: 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/Rtmpay7ED9/R.INSTALL1a3c6847436/erma/man/stateProfile.Rd:33: file link 'promoters' in package 'GenomicRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/erma.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 199.2Mb
sub-directories of 1Mb or more:
bed_tabix 161.4Mb
data 37.1Mb
* 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 ... NOTE
geneTxRange: no visible global function definition for 'select'
genemodelOLD: no visible binding for global variable 'exonsBy'
stateProfile: no visible binding for global variable 'states_25'
stateProfile: no visible binding for global variable 'short_celltype'
stateProfile: no visible binding for global variable 'name'
statesByRange: no visible binding for global variable 'mod'
statesByRange: no visible binding for global variable 'upstream'
statesByRange: no visible binding for global variable 'downstream'
statesByRange : <anonymous>: no visible binding for global variable
'tss'
statesByRange: no visible binding for global variable 'states_25'
Undefined global functions or variables:
downstream exonsBy mod name select short_celltype states_25 tss
upstream
* 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 ... NOTE
Failed with error: 'package 'DelayedArray' could not be loaded'
Error in .requirePackage(package) :
unable to find required package 'SummarizedExperiment'
Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
Execution halted
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
erma-package 9.39 0.50 29.25
stateProfile 3.30 0.14 22.50
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
erma-package 7.80 0.47 32.71
stateProfile 3.04 0.08 25.83
* 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-3.7-bioc/meat/erma.Rcheck/00check.log'
for details.
erma.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/erma_0.12.0.tar.gz && rm -rf erma.buildbin-libdir && mkdir erma.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=erma.buildbin-libdir erma_0.12.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL erma_0.12.0.zip && rm erma_0.12.0.tar.gz erma_0.12.0.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
19 197M 19 38.2M 0 0 94.8M 0 0:00:02 --:--:-- 0:00:02 96.3M
73 197M 73 144M 0 0 102M 0 0:00:01 0:00:01 --:--:-- 103M
100 197M 100 197M 0 0 99.8M 0 0:00:01 0:00:01 --:--:-- 100M
install for i386
* installing *source* package 'erma' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'erma'
finding HTML links ... done
ErmaSet-class html
finding level-2 HTML links ... done
erma-package html
genemodel html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpay7ED9/R.INSTALL1a3c6847436/erma/man/genemodel.Rd:46: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
mapmeta html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpay7ED9/R.INSTALL1a3c6847436/erma/man/mapmeta.Rd:21: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
stateProfile html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpay7ED9/R.INSTALL1a3c6847436/erma/man/stateProfile.Rd:33: file link 'promoters' in package 'GenomicRanges' does not exist and so has been treated as a topic
states_25 html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'erma' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'erma' as erma_0.12.0.zip
* DONE (erma)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'erma' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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erma.Rcheck/examples_i386/erma-Ex.timings
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erma.Rcheck/examples_x64/erma-Ex.timings
|