Thrash Adam
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/PAST |
| Branch: RELEASE_3_9 |
| Last Commit: bb44d41 |
| Last Changed Date: 2019-08-07 10:23:22 -0400 (Wed, 07 Aug 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:44:24 -0400 (Wed, 16 Oct 2019).
| Package 1171/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| PAST 1.0.1 Thrash Adam
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: PAST |
| Version: 1.0.1 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PAST.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings PAST_1.0.1.tar.gz |
| StartedAt: 2019-10-16 05:50:25 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:07:07 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 1001.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PAST.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PAST.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings PAST_1.0.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/PAST.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PAST/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PAST' version '1.0.1'
* package encoding: UTF-8
* 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 'PAST' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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
assign_SNPs_to_genes: no visible binding for global variable
'Marker_original.x'
find_pathway_significance: no visible binding for global variable
'gene_id'
load_GWAS_data: no visible binding for global variable 'Chr'
load_GWAS_data: no visible binding for global variable 'Pos'
Undefined global functions or variables:
Chr Marker_original.x Pos gene_id
* 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
plot_pathways 20.94 2.59 115.52
find_pathway_significance 19.25 2.89 127.79
assign_SNPs_to_genes 17.87 2.36 101.49
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plot_pathways 22.58 2.59 144.46
find_pathway_significance 21.06 2.58 133.92
assign_SNPs_to_genes 18.13 2.80 104.89
* 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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/PAST.Rcheck/00check.log'
for details.
PAST.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/PAST_1.0.1.tar.gz && rm -rf PAST.buildbin-libdir && mkdir PAST.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PAST.buildbin-libdir PAST_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL PAST_1.0.1.zip && rm PAST_1.0.1.tar.gz PAST_1.0.1.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 943k 100 943k 0 0 9642k 0 --:--:-- --:--:-- --:--:-- 10.2M
install for i386
* installing *source* package 'PAST' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'PAST'
finding HTML links ... done
assign_SNPs_to_genes html
assign_chunk html
determine_linkage html
find_pathway_significance html
find_representative_SNP html
find_representative_SNP_gene_pairing html
load_GWAS_data html
load_LD html
plot_pathways 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 'PAST' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PAST' as PAST_1.0.1.zip
* DONE (PAST)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'PAST' successfully unpacked and MD5 sums checked
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PAST.Rcheck/examples_i386/PAST-Ex.timings
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PAST.Rcheck/examples_x64/PAST-Ex.timings
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