Bioconductor Single Package Builder - Build History
nebbiolo1 Summary
Package: ReUseData |
Version: 0.99.18 |
RVersion: 4.3 |
BiocVersion: 3.17 |
BuildCommand: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ReUseData |
BuildTime: 0 minutes 53.98 seconds |
CheckCommand: BiocCheckGitClone('ReUseData') && /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2868/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2868/26f7022db2e479d0966c9f42c46a737fbb429f89/ReUseData.install-out.txt ReUseData_0.99.18.tar.gz && BiocCheck('ReUseData_0.99.18.tar.gz', `new-package`=TRUE) |
CheckTime: 2 minutes 33.98 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 581.75 KiB |
BuildID:: ReUseData_20230109201251 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: ReUseData. Starting Build package. Starting Check package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 1. |
nebbiolo1 BUILD SRC output
=============================== R CMD BUILD =============================== * checking for file ‘ReUseData/DESCRIPTION’ ... OK * preparing ‘ReUseData’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘ReUseData_0.99.18.tar.gz’
nebbiolo1 CHECK output
=============================== BiocCheckGitClone('ReUseData') =============================== ─ BiocCheckVersion: 1.35.9 ─ BiocVersion: 3.17 ─ Package: ReUseData ─ PackageVersion: 0.99.18 ─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2868/26f7022db2e479d0966c9f42c46a737fbb429f89/ReUseData ─ platform: unix ─ isTarBall: FALSE * Checking valid files... * Checking for stray BiocCheck output folders... * Checking for inst/doc folders... * Checking DESCRIPTION... * Checking if DESCRIPTION is well formatted... * Checking for valid maintainer... * Checking CITATION... ─ BiocCheck results ── 0 ERRORS | 0 WARNINGS | 0 NOTES For more details, run browseVignettes(package = 'BiocCheck') =============================== R CMD CHECK =============================== * using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2868/26f7022db2e479d0966c9f42c46a737fbb429f89/ReUseData.Rcheck’ * using R Under development (unstable) (2022-12-10 r83428) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ReUseData/DESCRIPTION’ ... OK * this is package ‘ReUseData’ version ‘0.99.18’ * 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 serialization versions ... OK * checking whether package ‘ReUseData’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... 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 ... [4s/4s] OK * checking whether the package can be loaded with stated dependencies ... [4s/4s] OK * checking whether the package can be unloaded cleanly ... [4s/4s] OK * checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK * checking whether the namespace can be unloaded cleanly ... [4s/4s] OK * checking loading without being on the library search path ... [4s/4s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... NOTE ':::' call which should be '::': ‘Rcwl:::env_Rcwl’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [15s/15s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... 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 files in ‘vignettes’ ... OK * checking examples ... [39s/40s] OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed dataUpdate 9.152 0.397 9.617 getCloudData 7.089 0.172 8.343 dataHub-class 5.667 0.308 6.206 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [22s/23s] [22s/23s] 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 ... [3s/3s] OK * DONE Status: 1 NOTE See ‘/home/pkgbuild/packagebuilder/workers/jobs/2868/26f7022db2e479d0966c9f42c46a737fbb429f89/ReUseData.Rcheck/00check.log’ for details. =============================== BiocCheck('ReUseData_0.99.18.tar.gz') =============================== ─ BiocCheckVersion: 1.35.9 ─ BiocVersion: 3.17 ─ Package: ReUseData ─ PackageVersion: 0.99.18 ─ sourceDir: /tmp/Rtmp2lwCyP/file1d5d752dce7b71/ReUseData ─ installDir: /tmp/Rtmp2lwCyP/file1d5d7523475b6 ─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2868/26f7022db2e479d0966c9f42c46a737fbb429f89/ReUseData.BiocCheck ─ platform: unix ─ isTarBall: TRUE * Installing package... * Checking for deprecated package usage... * Checking for remote package usage... * Checking for 'LazyData: true' usage... * Checking version number... * Checking for version number mismatch... * Checking new package version number... * Checking R version dependency... * Checking package size... * Checking individual file sizes... * Checking biocViews... * Checking that biocViews are present... * Checking package type based on biocViews... Software * Checking for non-trivial biocViews... * Checking that biocViews come from the same category... * Checking biocViews validity... * Checking for recommended biocViews... * NOTE: Consider adding these automatically suggested biocViews: WorkflowManagement Search 'biocViews' at https://contributions.bioconductor.org * Checking build system compatibility... * Checking for blank lines in DESCRIPTION... * Checking if DESCRIPTION is well formatted... * Checking for proper Description: field... * Checking for whitespace in DESCRIPTION field names... * Checking that Package field matches directory/tarball name... * Checking for Version field... * Checking for valid maintainer... * Checking License: for restrictive use... * NOTE: License 'GPL (>= 3)' unknown; licenses cannot restrict use * Checking for pinned package versions... * Checking DESCRIPTION/NAMESPACE consistency... * Checking .Rbuildignore... * Checking for stray BiocCheck output folders... * Checking vignette directory... * Checking whether vignette is built with 'R CMD build'... * Checking package installation calls in R code... * Checking for library/require of ReUseData... * Checking coding practice... * NOTE: Avoid sapply(); use vapply() * NOTE: Avoid 'cat' and 'print' outside of 'show' methods * NOTE: Avoid using '=' for assignment and use '<-' instead * NOTE: Avoid the use of 'paste' in condition signals * NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions * ERROR: Avoid references to external hosting platforms * Checking parsed R code in R directory, examples, vignettes... * Checking function lengths... * NOTE: The recommended function length is 50 lines or less. There are 41 functions greater than 50 lines. * Checking man page documentation... * NOTE: Consider adding runnable examples to man pages that document exported objects. * NOTE: Usage of dontrun{} / donttest{} tags found in man page examples. 36% of man pages use at least one of these tags. * NOTE: Use donttest{} instead of dontrun{}. * Checking package NEWS... * NOTE: Consider adding a NEWS file, so your package news will be included in Bioconductor release announcements. * Checking unit tests... * Checking skip_on_bioc() in tests... * Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vignette source... * NOTE: Consider shorter lines; 46 lines (2%) are > 80 characters long. * NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain tabs. * NOTE: Consider multiples of 4 spaces for line indents; 126 lines (5%) are not. See https://contributions.bioconductor.org/r-code.html See styler package: https://cran.r-project.org/package=styler as described in the BiocCheck vignette. * Checking if package already exists in CRAN... * Checking if new package already exists in Bioconductor... * Checking for bioc-devel mailing list subscription... Maintainer is subscribed to bioc-devel. * Checking for support site registration... Maintainer is registered at support site. Package name is in support site watched tags. ─ BiocCheck results ── 1 ERRORS | 0 WARNINGS | 15 NOTES See the ReUseData.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details.
nebbiolo1 BUILD BIN output
merida1 Summary
Package: ReUseData |
Version: 0.99.18 |
RVersion: 4.3 |
BiocVersion: 3.17 |
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ReUseData |
BuildTime: 1 minutes 59.69 seconds |
CheckCommand: BiocCheckGitClone('ReUseData') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/2868/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/2868/26f7022db2e479d0966c9f42c46a737fbb429f89/ReUseData.install-out.txt ReUseData_0.99.18.tar.gz && BiocCheck('ReUseData_0.99.18.tar.gz', `new-package`=TRUE) |
CheckTime: 4 minutes 29.56 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh ReUseData_0.99.18.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 4.81 seconds |
PackageFileSize: 581.20 KiB |
BuildID:: ReUseData_20230109201251 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: ReUseData. Starting Build package. Starting Check package. Starting Build package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 1. Build Package status: 1. |
merida1 BUILD SRC output
=============================== R CMD BUILD =============================== * checking for file ‘ReUseData/DESCRIPTION’ ... OK * preparing ‘ReUseData’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘ReUseData_0.99.18.tar.gz’
merida1 CHECK output
=============================== BiocCheckGitClone('ReUseData') =============================== ─ BiocCheckVersion: 1.35.9 ─ BiocVersion: 3.17 ─ Package: ReUseData ─ PackageVersion: 0.99.18 ─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2868/26f7022db2e479d0966c9f42c46a737fbb429f89/ReUseData ─ platform: unix ─ isTarBall: FALSE * Checking valid files... * Checking for stray BiocCheck output folders... * Checking for inst/doc folders... * Checking DESCRIPTION... * Checking if DESCRIPTION is well formatted... * Checking for valid maintainer... * Checking CITATION... ─ BiocCheck results ── 0 ERRORS | 0 WARNINGS | 0 NOTES For more details, run browseVignettes(package = 'BiocCheck') =============================== R CMD CHECK =============================== * using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2868/26f7022db2e479d0966c9f42c46a737fbb429f89/ReUseData.Rcheck’ * using R Under development (unstable) (2022-12-10 r83428) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ReUseData/DESCRIPTION’ ... OK * this is package ‘ReUseData’ version ‘0.99.18’ * 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 serialization versions ... OK * checking whether package ‘ReUseData’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... 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 ... [9s/10s] OK * checking whether the package can be loaded with stated dependencies ... [8s/9s] OK * checking whether the package can be unloaded cleanly ... [8s/9s] OK * checking whether the namespace can be loaded with stated dependencies ... [8s/9s] OK * checking whether the namespace can be unloaded cleanly ... [9s/10s] OK * checking loading without being on the library search path ... [9s/10s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... NOTE ':::' call which should be '::': ‘Rcwl:::env_Rcwl’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [35s/39s] OK * checking Rd files ... [1s/1s] OK * checking Rd metadata ... OK * checking Rd line widths ... 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 files in ‘vignettes’ ... OK * checking examples ... [38s/42s] ERROR Running examples in ‘ReUseData-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: dataUpdate > ### Title: dataUpdate > ### Aliases: dataUpdate > > ### ** Examples > > ## Generate data > library(Rcwl) Loading required package: yaml Loading required package: S4Vectors Loading required package: stats4 Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:base’: I, expand.grid, unname > outdir <- file.path(tempdir(), "SharedData") > > recipeLoad("echo_out", return = TRUE) Data recipe 'echo_out' loaded! Use inputs(echo_out) to check required input parameters before evaluation. Check here: https://rcwl.org/dataRecipes/echo_out.html for user instructions (e.g., eligible input values, data source, etc.) > Rcwl::inputs(echo_out) inputs: input (input) (string): outfile (outfile) (string): > echo_out$input <- "Hello World!" > echo_out$outfile <- "outfile" > res <- getData(echo_out, + outdir = outdir, + notes = c("echo", "hello", "world", "txt"), + showLog = TRUE) [1;30mINFO[0m /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/Rcwl/1.15.5/env_Rcwl/bin/cwltool 3.1.20221201130942 [1;30mINFO[0m Resolved '/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpeRVKsi/SharedData/echo_out_Hello_World!_outfile.cwl' to 'file:///var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/RtmpeRVKsi/SharedData/echo_out_Hello_World%21_outfile.cwl' [1;30mINFO[0m [job echo_out_Hello_World%21_outfile.cwl] /private/tmp/docker_tmpm_4ye2g1$ bash \ script.sh \ 'Hello World!' \ outfile [1;30mINFO[0m [job echo_out_Hello_World%21_outfile.cwl] completed success [1;30mINFO[0m Final process status is success } > > ## Not run: > ##D recipeLoad("ensembl_liftover", return = TRUE) > ##D Rcwl::inputs(ensembl_liftover) > ##D ensembl_liftover$species <- "human" > ##D ensembl_liftover$from <- "GRCh37" > ##D ensembl_liftover$to <- "GRCh38" > ##D res <- getData(ensembl_liftover, > ##D outdir = outdir, > ##D notes = c("ensembl", "liftover", "human", "GRCh37", "GRCh38"), > ##D showLog = TRUE) > ## End(Not run) > ## Update data cache (with or without pre-built data sets from ReUseData cloud bucket) > dataUpdate(dir = outdir) Warning in read.dcf(file.path(p, "DESCRIPTION"), c("Package", "Version")) : cannot open compressed file '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BiocFileCache/DESCRIPTION', probable reason 'No such file or directory' Warning in file(con, "r") : file("") only supports open = "w+" and open = "w+b": using the former Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'mcols': attempt to select less than one element in get1index Calls: dataUpdate ... .get_all_rids -> .sql_cmd -> paste -> .handleSimpleError -> h Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [1s/1s] [1s/1s] ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(ReUseData) Error: package or namespace load failed for 'ReUseData' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called 'BiocFileCache' Execution halted * 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 ... [9s/11s] OK * DONE Status: 2 ERRORs, 1 NOTE See ‘/Users/pkgbuild/packagebuilder/workers/jobs/2868/26f7022db2e479d0966c9f42c46a737fbb429f89/ReUseData.Rcheck/00check.log’ for details. =============================== BiocCheck('ReUseData_0.99.18.tar.gz') =============================== cmd: /Library/Frameworks/R.framework/Resources/bin/R args: --vanilla CMD INSTALL --no-test-load --library=/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpQ5lsxQ/file305c453dcccf/lib '/Users/pkgbuild/packagebuilder/workers/jobs/2868/26f7022db2e479d0966c9f42c46a737fbb429f89/ReUseData_0.99.18.tar.gz' stderr: * installing *source* package ‘ReUseData’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ERROR: lazy loading failed for package ‘ReUseData’ * removing ‘/private/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/RtmpQ5lsxQ/file305c453dcccf/lib/ReUseData’ * ERROR: /Users/pkgbuild/packagebuilder/workers/jobs/2868/26f7022db2e479d0966c9f42c46a737fbb429f89/ReUseData_0.99.18.tar.gz must be installable. cmd: /Library/Frameworks/R.framework/Resources/bin/R args: --vanilla -e 'library(ReUseData)' stderr: Error: package or namespace load failed for ‘ReUseData’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘BiocParallel’ Execution halted * ERROR: /Users/pkgbuild/packagebuilder/workers/jobs/2868/26f7022db2e479d0966c9f42c46a737fbb429f89/ReUseData_0.99.18.tar.gz must be loadable. ─ BiocCheckVersion: 1.35.9 ─ BiocVersion: 3.17 ─ Package: ReUseData ─ PackageVersion: 0.99.18 ─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpQ5lsxQ/file305c412d95be/ReUseData ─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpQ5lsxQ/file305c453dcccf ─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2868/26f7022db2e479d0966c9f42c46a737fbb429f89/ReUseData.BiocCheck ─ platform: unix ─ isTarBall: TRUE * Installing package... * Checking for deprecated package usage... * Checking for remote package usage... * Checking for 'LazyData: true' usage... * Checking version number... * Checking for version number mismatch... * Checking new package version number... * Checking R version dependency... * Checking package size... * Checking individual file sizes... * Checking biocViews... * Checking that biocViews are present... * Checking package type based on biocViews... Software * Checking for non-trivial biocViews... * Checking that biocViews come from the same category... * Checking biocViews validity... * Checking for recommended biocViews... * NOTE: Consider adding these automatically suggested biocViews: WorkflowManagement Search 'biocViews' at https://contributions.bioconductor.org * Checking build system compatibility... * Checking for blank lines in DESCRIPTION... * Checking if DESCRIPTION is well formatted... * Checking for proper Description: field... * Checking for whitespace in DESCRIPTION field names... * Checking that Package field matches directory/tarball name... * Checking for Version field... * Checking for valid maintainer... * Checking License: for restrictive use... * NOTE: License 'GPL (>= 3)' unknown; licenses cannot restrict use * Checking for pinned package versions... * Checking DESCRIPTION/NAMESPACE consistency... Warning in packageDescription(pkgname, lib.loc = lib.loc) : no package 'ReUseData' was found Error in pkg_desc$Imports : $ operator is invalid for atomic vectors Calls: BiocCheck ... checkDescriptionNamespaceConsistency -> cleanupDependency Execution halted
merida1 BUILD BIN output
=============================== R CMD BUILD =============================== >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir ReUseData_0.99.18.tar.gz' >>>>>>> * installing *source* package ‘ReUseData’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : there is no package called ‘BiocParallel’ Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted ERROR: lazy loading failed for package ‘ReUseData’ * removing ‘/Users/pkgbuild/packagebuilder/workers/jobs/2868/26f7022db2e479d0966c9f42c46a737fbb429f89/libdir/ReUseData’