Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:14:52 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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To the developers/maintainers of the bioCancer package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bioCancer.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 156/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
bioCancer 1.27.0 (landing page) Karim Mezhoud
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: bioCancer |
Version: 1.27.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:bioCancer.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings bioCancer_1.27.0.tar.gz |
StartedAt: 2023-02-06 18:45:24 -0000 (Mon, 06 Feb 2023) |
EndedAt: 2023-02-06 18:51:03 -0000 (Mon, 06 Feb 2023) |
EllapsedTime: 338.5 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: bioCancer.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:bioCancer.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings bioCancer_1.27.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/bioCancer.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 ‘bioCancer/DESCRIPTION’ ... OK * this is package ‘bioCancer’ version ‘1.27.0’ * 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 ‘bioCancer’ can be installed ... OK * checking installed package size ... NOTE installed size is 5.7Mb sub-directories of 1Mb or more: app 3.4Mb extdata 1.6Mb * 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: metamorphosis: bioCancer is a radiant.data extension Cannot process chunk/lines: reduce size of package by half 14 -> 7 mb Cannot process chunk/lines: improve Reactome_ui functions Cannot process chunk/lines: add switch button to ui_circomics Cannot process chunk/lines: improve circomics functions Cannot process chunk/lines: delete commented files and figures Cannot process chunk/lines: cleanup ui_radiant, /Rbis, /quant, /bioCancer Cannot process chunk/lines: switchButton Cannot process chunk/lines: data.row.names(row.names, rowsi, i) : Cannot process chunk/lines: some row.names duplicated: 11,12,13,14 --> row.names NOT used Cannot process chunk/lines: dplyr::mutate_each() is deprecated Cannot process chunk/lines: dply::summarise_each() is deprecated Cannot process chunk/lines: replace BiocStyle by prettydoc Cannot process chunk/lines: Warning in formals(fun) : argument is not a function Cannot process chunk/lines: Warning in body(fun) : argument is not a function Cannot process chunk/lines: Fix setting plot size Cannot process chunk/lines: Change the color rang of Circular layout plot as in standards Cannot process chunk/lines: update Correlation Methods Cannot process chunk/lines: replace .libPath() by path.package('bioCancer') in portal.R file * 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 ... NOTE Namespaces in Imports field not imported from: ‘AlgDesign’ ‘GO.db’ ‘R.methodsS3’ ‘import’ ‘methods’ ‘org.Bt.eg.db’ ‘shinythemes’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE getGenesClassification: no visible global function definition for ‘new’ Undefined global functions or variables: new Consider adding importFrom("methods", "new") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘bioCancer-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: getProfileData.CGDS > ### Title: S3 method to get Profile Data > ### Aliases: getProfileData.CGDS > > ### ** Examples > > # Create CGDS object > mycgds <- CGDS("http://www.cbioportal.org/") > # Get list of cancer studies at server > mycancerstudy <- getCancerStudies.CGDS(mycgds)[2,1] > # Get available case lists (collection of samples) for a given cancer study > mycaselist <- getCaseLists.CGDS(mycgds,mycancerstudy)[1,1] Error in curl::curl_fetch_memory(url, handle = handle) : Empty reply from server Calls: getCaseLists.CGDS ... request_fetch -> request_fetch.write_memory -> <Anonymous> Execution halted * 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 ... ‘bioCancer.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 4 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/bioCancer.Rcheck/00check.log’ for details.
bioCancer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL bioCancer ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘bioCancer’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** 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 (bioCancer)
bioCancer.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-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(bioCancer) Loading required package: radiant.data Loading required package: magrittr Attaching package: 'magrittr' The following objects are masked from 'package:testthat': equals, is_less_than, not Loading required package: ggplot2 Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: tidyr Attaching package: 'tidyr' The following object is masked from 'package:magrittr': extract The following object is masked from 'package:testthat': matches Loading required package: dplyr Attaching package: 'dplyr' The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Attaching package: 'radiant.data' The following objects are masked from 'package:lubridate': month, wday The following object is masked from 'package:ggplot2': diamonds The following object is masked from 'package:magrittr': set_attr The following object is masked from 'package:testthat': describe The following object is masked from 'package:base': date Loading required package: XML > > test_check("bioCancer") getCancerStudies... OK getCaseLists (1/2) ... OK getCaseLists (2/2) ... OK getGeneticProfiles (1/2) ... OK getGeneticProfiles (2/2) ... OK getClinicalData (1/1) ... OK getProfileData (1/6) ... OK getProfileData (2/6) ... OK getProfileData (3/6) ... OK getProfileData (4/6) ... OK getProfileData (5/6) ... OK getProfileData (6/6) ... OK ReactomeFI connection... OK [ FAIL 0 | WARN 0 | SKIP 2 | PASS 0 ] ══ Skipped tests ═══════════════════════════════════════════════════════════════ • empty test (2) [ FAIL 0 | WARN 0 | SKIP 2 | PASS 0 ] > > proc.time() user system elapsed 12.588 0.392 22.622
bioCancer.Rcheck/bioCancer-Ex.timings
name | user | system | elapsed | |
AnnotationFuncs-package | 0.422 | 0.012 | 0.745 | |
Edges_Diseases_obj | 0.001 | 0.002 | 0.002 | |
Mutation_obj | 0 | 0 | 0 | |
Node_Diseases_obj | 0.002 | 0.000 | 0.002 | |
Node_df_FreqIn | 0.001 | 0.000 | 0.001 | |
Node_obj_CNA_ProfData | 0.000 | 0.000 | 0.001 | |
Node_obj_FreqIn | 0.001 | 0.000 | 0.001 | |
Node_obj_Met_ProfData | 0 | 0 | 0 | |
Node_obj_mRNA_Classifier | 0.001 | 0.000 | 0.000 | |
Studies_obj | 0.008 | 0.000 | 0.008 | |
UnifyRowNames | 0 | 0 | 0 | |
attriColorGene | 0 | 0 | 0 | |
attriColorValue | 0 | 0 | 0 | |
attriColorVector | 0.001 | 0.000 | 0.001 | |
attriShape2Gene | 0 | 0 | 0 | |
attriShape2Node | 0 | 0 | 0 | |
bioCancer | 0 | 0 | 0 | |
checkDimensions | 0 | 0 | 0 | |
coffeewheel | 0 | 0 | 0 | |
coffeewheelOutput | 0 | 0 | 0 | |
displayTable | 0 | 0 | 0 | |
findPhantom | 0 | 0 | 0 | |
getCancerStudies.CGDS | 0.053 | 0.009 | 1.123 | |
getCaseLists.CGDS | 0.028 | 0.000 | 1.174 | |
getClinicalData.CGDS | 0.715 | 0.000 | 2.375 | |
getEvidenceCodes | 0.001 | 0.000 | 0.000 | |
getFreqMutData | 0 | 0 | 0 | |
getGenesClassification | 0.000 | 0.000 | 0.001 | |
getGeneticProfiles.CGDS | 0.051 | 0.000 | 3.399 | |
getListProfData | 0 | 0 | 0 | |
getList_Cases | 0.000 | 0.000 | 0.001 | |
getList_GenProfs | 0 | 0 | 0 | |
getMegaProfData | 0 | 0 | 0 | |
getMutationData.CGDS | 0.014 | 0.000 | 0.526 | |
getOrthologs | 0 | 0 | 0 | |