| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:46 -0000 (Wed, 01 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the PAST package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PAST.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1430/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PAST 1.15.0 (landing page) Thrash Adam
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: PAST |
| Version: 1.15.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:PAST.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings PAST_1.15.0.tar.gz |
| StartedAt: 2023-02-28 10:49:03 -0000 (Tue, 28 Feb 2023) |
| EndedAt: 2023-02-28 11:10:37 -0000 (Tue, 28 Feb 2023) |
| EllapsedTime: 1293.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: PAST.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:PAST.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings PAST_1.15.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/PAST.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘PAST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PAST’ version ‘1.15.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘PAST’ can be installed ... WARNING
Found the following significant warnings:
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::intersect’ by ‘dplyr::intersect’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::union’ by ‘dplyr::union’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::setdiff’ by ‘dplyr::setdiff’ 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 ‘/home/biocbuild/bbs-3.17-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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_pathways 9.411 1.491 293.257
find_pathway_significance 9.458 0.701 266.153
assign_SNPs_to_genes 7.628 0.273 210.488
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘past.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/PAST.Rcheck/00check.log’
for details.
PAST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL PAST ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘PAST’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading 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::intersect’ by ‘dplyr::intersect’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::union’ by ‘dplyr::union’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::setdiff’ by ‘dplyr::setdiff’ 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 ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location 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::intersect’ by ‘dplyr::intersect’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::union’ by ‘dplyr::union’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::setdiff’ by ‘dplyr::setdiff’ 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::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::intersect’ by ‘dplyr::intersect’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::union’ by ‘dplyr::union’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::setdiff’ by ‘dplyr::setdiff’ 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 * DONE (PAST)
PAST.Rcheck/PAST-Ex.timings
| name | user | system | elapsed | |
| assign_SNPs_to_genes | 7.628 | 0.273 | 210.488 | |
| find_pathway_significance | 9.458 | 0.701 | 266.153 | |
| load_GWAS_data | 0.285 | 0.004 | 0.289 | |
| load_LD | 0.573 | 0.028 | 0.601 | |
| plot_pathways | 9.411 | 1.491 | 293.257 | |