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This page was generated on 2021-08-03 12:05:51 -0400 (Tue, 03 Aug 2021).

CHECK results for PFP on nebbiolo2

To the developers/maintainers of the PFP package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PFP.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1357/2015HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PFP 1.1.0  (landing page)
XC Zhang
Snapshot Date: 2021-08-02 14:50:09 -0400 (Mon, 02 Aug 2021)
URL: https://git.bioconductor.org/packages/PFP
Branch: master
Last Commit: a3e8d80
Last Changed Date: 2021-05-19 12:58:46 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  NO, package depends on 'KEGGgraph' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: PFP
Version: 1.1.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:PFP.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings PFP_1.1.0.tar.gz
StartedAt: 2021-08-02 20:41:17 -0400 (Mon, 02 Aug 2021)
EndedAt: 2021-08-02 20:44:42 -0400 (Mon, 02 Aug 2021)
EllapsedTime: 205.6 seconds
RetCode: 0
Status:   OK  
CheckDir: PFP.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:PFP.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings PFP_1.1.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/PFP.Rcheck’
* using R version 4.1.0 beta (2021-05-03 r80259)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PFP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PFP’ version ‘1.1.0’
* 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 ‘PFP’ 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 ... 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 ... OK
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
calc_PFP_score 12.96  0.063  13.025
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: OK


Installation output

PFP.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL PFP
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘PFP’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (PFP)

Tests output

PFP.Rcheck/tests/testthat.Rout


R version 4.1.0 beta (2021-05-03 r80259) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(PFP)

> test_check('PFP')
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 31 ]
> 
> proc.time()
   user  system elapsed 
  7.999   0.350   8.335 

Example timings

PFP.Rcheck/PFP-Ex.timings

nameusersystemelapsed
PFP-class0.1110.0240.135
PFPRefnet-class0.5160.0280.544
PFPRefnet_hsa0.2990.0000.299
PFPRefnet_mmu0.3720.0150.388
PFP_score-methods0.0040.0000.004
PFP_test10.0040.0000.005
PFP_test20.0040.0000.005
calc_PFP_score12.960 0.06313.025
data_std0.010.000.01
gene_list_hsa0.0010.0000.000
genes_score-methods0.0040.0000.004
get_PFPRefnet0.0000.0000.001
get_asso_net1.6350.0031.640
get_bg_related_kegg1.6810.0001.681
get_exp_cor_edges0.1030.0070.111
get_pathway_info0.1070.0163.633
group-methods0.3010.0120.313
kegg_download000
net_info-methods0.3390.0200.359
net_names-methods0.2970.0000.298
network-methods0.2970.0040.301
pathway_info0.0020.0000.002
pathway_info_hsa0.0010.0000.001
pathways_score-methods0.0000.0040.004
plot_PFP-methods0.3410.0120.353
plot_PFPlist0.1750.0000.175
rank_PFP-methods0.1270.0160.143
refnet_info-methods0.0040.0000.004
refnet_names-methods0.0040.0000.004
result_PFP-methods0.0060.0000.005
show_PFP-methods0.0040.0020.006
show_net-methods0.2780.0010.279
stats_test-methods0.0040.0000.004
sub_PFP-methods0.1180.0240.142
subnet-methods0.3030.0000.303
trans_edges_id2.6270.0842.711
trans_graph2PFPRefnet0.4600.0240.484
trans_xml2graph0.0000.0000.001