| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:38 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 | ||||
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To the developers/maintainers of the PAST package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1452/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PAST 1.17.0 (landing page) Thrash Adam
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: PAST |
| Version: 1.17.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:PAST.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings PAST_1.17.0.tar.gz |
| StartedAt: 2023-06-06 03:53:28 -0000 (Tue, 06 Jun 2023) |
| EndedAt: 2023-06-06 04:06:17 -0000 (Tue, 06 Jun 2023) |
| EllapsedTime: 769.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: PAST.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:PAST.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings PAST_1.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/PAST.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘PAST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PAST’ version ‘1.17.0’
* 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::findMatches’ by ‘utils::findMatches’ 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-3.18-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 loading without being on the library search path ... 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 7.894 0.614 126.856
find_pathway_significance 6.613 0.918 132.169
assign_SNPs_to_genes 6.131 0.205 87.156
* 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-3.18-bioc/meat/PAST.Rcheck/00check.log’
for details.
PAST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL PAST ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-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::findMatches’ by ‘utils::findMatches’ 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::findMatches’ by ‘utils::findMatches’ 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::findMatches’ by ‘utils::findMatches’ 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 | 6.131 | 0.205 | 87.156 | |
| find_pathway_significance | 6.613 | 0.918 | 132.169 | |
| load_GWAS_data | 0.244 | 0.020 | 0.265 | |
| load_LD | 0.640 | 0.084 | 0.725 | |
| plot_pathways | 7.894 | 0.614 | 126.856 | |