Thrash Adam
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/PAST |
| Branch: RELEASE_3_12 |
| Last Commit: eefb1b4 |
| Last Changed Date: 2020-10-27 11:46:25 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:32:41 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the PAST package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1301/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PAST 1.6.0 (landing page) Thrash Adam
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: PAST |
| Version: 1.6.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PAST.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings PAST_1.6.0.tar.gz |
| StartedAt: 2021-05-06 05:22:39 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 05:39:41 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 1022.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: PAST.Rcheck |
| Warnings: 2 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PAST.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings PAST_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/PAST.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.6.0'
* 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 ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'S4Vectors::union' by 'dplyr::union' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::intersect' by 'dplyr::intersect' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::setdiff' by 'dplyr::setdiff' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::first' by 'dplyr::first' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::setequal' by 'dplyr::setequal' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::rename' by 'dplyr::rename' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::tail' by 'utils::tail' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::stack' by 'utils::stack' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::head' by 'utils::head' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::complete.cases' by 'stats::complete.cases' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::sd' by 'stats::sd' when loading 'PAST'
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/PAST.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 ... NOTE
assign_SNPs_to_genes: no visible binding for global variable 'position'
assign_SNPs_to_genes: no visible binding for global variable
'Marker_original'
assign_SNPs_to_genes: no visible binding for global variable 'effect'
assign_SNPs_to_genes: no visible binding for global variable 'p.value'
assign_SNPs_to_genes: no visible binding for global variable
'linked_snp_count'
assign_SNPs_to_genes: no visible binding for global variable 'name'
assign_SNPs_to_genes: no visible binding for global variable 'marker'
assign_chunk: no visible binding for global variable 'chromosome'
assign_chunk: no visible global function definition for 'IRanges'
assign_chunk: no visible binding for global variable 'position'
assign_chunk: no visible binding for global variable 'seqid'
assign_chunk: no visible binding for global variable 'Name'
find_pathway_significance: no visible binding for global variable
'gene_id'
plot_pathways: no visible binding for global variable
'running_enrichment_score'
Undefined global functions or variables:
IRanges Marker_original Name chromosome effect gene_id
linked_snp_count marker name p.value position
running_enrichment_score seqid
* 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 ... WARNING
Undocumented arguments in documentation object 'assign_SNPs_to_genes'
'filter_type'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 (user + system) or elapsed time > 5s
user system elapsed
plot_pathways 9.31 1.03 129.74
find_pathway_significance 6.27 0.43 125.83
assign_SNPs_to_genes 4.84 0.68 79.81
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
find_pathway_significance 8.11 0.37 139.97
plot_pathways 6.67 0.33 137.78
assign_SNPs_to_genes 5.91 0.28 86.64
* 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 WARNINGs, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/PAST.Rcheck/00check.log'
for details.
PAST.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/PAST_1.6.0.tar.gz && rm -rf PAST.buildbin-libdir && mkdir PAST.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PAST.buildbin-libdir PAST_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL PAST_1.6.0.zip && rm PAST_1.6.0.tar.gz PAST_1.6.0.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 944k 100 944k 0 0 37.7M 0 --:--:-- --:--:-- --:--:-- 40.0M
install for i386
* installing *source* package 'PAST' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'S4Vectors::union' by 'dplyr::union' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::intersect' by 'dplyr::intersect' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::setdiff' by 'dplyr::setdiff' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::first' by 'dplyr::first' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::setequal' by 'dplyr::setequal' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::rename' by 'dplyr::rename' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::tail' by 'utils::tail' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::stack' by 'utils::stack' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::head' by 'utils::head' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::complete.cases' by 'stats::complete.cases' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::sd' by 'stats::sd' when loading 'PAST'
** 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
Warning: replacing previous import 'S4Vectors::union' by 'dplyr::union' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::intersect' by 'dplyr::intersect' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::setdiff' by 'dplyr::setdiff' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::first' by 'dplyr::first' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::setequal' by 'dplyr::setequal' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::rename' by 'dplyr::rename' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::tail' by 'utils::tail' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::stack' by 'utils::stack' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::head' by 'utils::head' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::complete.cases' by 'stats::complete.cases' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::sd' by 'stats::sd' when loading 'PAST'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'S4Vectors::union' by 'dplyr::union' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::intersect' by 'dplyr::intersect' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::setdiff' by 'dplyr::setdiff' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::first' by 'dplyr::first' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::setequal' by 'dplyr::setequal' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::rename' by 'dplyr::rename' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::tail' by 'utils::tail' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::stack' by 'utils::stack' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::head' by 'utils::head' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::complete.cases' by 'stats::complete.cases' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::sd' by 'stats::sd' when loading 'PAST'
** 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
Warning: replacing previous import 'S4Vectors::union' by 'dplyr::union' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::intersect' by 'dplyr::intersect' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::setdiff' by 'dplyr::setdiff' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::first' by 'dplyr::first' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::setequal' by 'dplyr::setequal' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::rename' by 'dplyr::rename' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::tail' by 'utils::tail' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::stack' by 'utils::stack' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::head' by 'utils::head' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::complete.cases' by 'stats::complete.cases' when loading 'PAST'
Warning: replacing previous import 'S4Vectors::sd' by 'stats::sd' when loading 'PAST'
* MD5 sums
packaged installation of 'PAST' as PAST_1.6.0.zip
* DONE (PAST)
* installing to library 'C:/Users/biocbuild/bbs-3.12-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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