Bioconductor Single Package Builder - Build History
nebbiolo1 Summary
Package: spoon |
Version: 0.99.7 |
RVersion: 4.4 |
BiocVersion: 3.19 |
BuildCommand: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data spoon |
BuildTime: 1 minutes 56.49 seconds |
CheckCommand: BiocCheckGitClone('spoon') && /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3278/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3278/a4ae8270604c41fd1e7f2c0f00bd2b3ba3cd87f6/spoon.install-out.txt spoon_0.99.7.tar.gz && BiocCheck('spoon_0.99.7.tar.gz', `new-package`=TRUE) |
CheckTime: 2 minutes 44.48 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 813.54 KiB |
BuildID:: spoon_20240221195521 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: spoon. 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. Adding Build Product Information to Database.Checking Package status: 1. |
nebbiolo1 BUILD SRC output
=============================== R CMD BUILD =============================== * checking for file spoon/DESCRIPTION ... OK * preparing spoon: * 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 spoon_0.99.7.tar.gz
nebbiolo1 CHECK output
=============================== BiocCheckGitClone('spoon') =============================== BiocCheckVersion: 1.39.26 BiocVersion: 3.19 Package: spoon PackageVersion: 0.99.7 sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3278/a4ae8270604c41fd1e7f2c0f00bd2b3ba3cd87f6/spoon 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... * NOTE: (Optional) CITATION file not found. Only include a CITATION file if there is a preprint or publication for this Bioconductor package. Note that Bioconductor packages are not required to have a CITATION file but it is useful both for users and for tracking Bioconductor project-wide metrics. When including a CITATION file, add the publication using the 'doi' argument of 'bibentry()'. BiocCheck results 0 ERRORS | 0 WARNINGS | 1 NOTES For more details, run browseVignettes(package = 'BiocCheck') =============================== R CMD CHECK =============================== * using log directory /home/pkgbuild/packagebuilder/workers/jobs/3278/a4ae8270604c41fd1e7f2c0f00bd2b3ba3cd87f6/spoon.Rcheck * using R Under development (unstable) (2024-01-16 r85808) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * using option --no-vignettes * checking for file spoon/DESCRIPTION ... OK * this is package spoon version 0.99.7 * 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 spoon 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 ... NOTE License stub is invalid DCF. * 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 ... [7s/7s] OK * checking whether the package can be loaded with stated dependencies ... [7s/7s] OK * checking whether the package can be unloaded cleanly ... [7s/7s] OK * checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK * checking whether the namespace can be unloaded cleanly ... [7s/7s] OK * checking loading without being on the library search path ... [7s/7s] OK * checking use of S3 registration ... 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 ... [23s/23s] 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 ... WARNING Error: package or namespace load failed for spoon in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called zlibbioc Call sequence: 6: stop(msg, call. = FALSE, domain = NA) 5: value[[3L]](cond) 4: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 3: tryCatchList(expr, classes, parentenv, handlers) 2: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps, exclude, include.only) }, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return && !quietly) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA) }) 1: library(package, lib.loc = lib.loc, character.only Execution halted * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in vignettes ... OK * checking examples ... [10s/10s] ERROR Running examples in spoon-Ex.R failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: generate_weights > ### Title: Generate weights > ### Aliases: generate_weights > > ### ** Examples > > library(nnSVG) > library(STexampleData) Loading required package: ExperimentHub 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, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: AnnotationHub Loading required package: BiocFileCache Loading required package: dbplyr Loading required package: SpatialExperiment Loading required package: SingleCellExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: MatrixGenerics The following objects are masked from package:matrixStats: colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: S4Vectors Attaching package: S4Vectors The following object is masked from package:utils: findMatches The following objects are masked from package:base: I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Error: package Biobase required by SummarizedExperiment could not be found Execution halted * checking for unstated dependencies in tests ... OK * checking tests ... Running testthat.R [4s/4s] [4s/4s] ERROR Running the tests in tests/testthat.R failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(spoon) Error: package or namespace load failed for 'spoon' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called 'Biobase' Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... [2s/2s] OK * DONE Status: 2 ERRORs, 1 WARNING, 1 NOTE See /home/pkgbuild/packagebuilder/workers/jobs/3278/a4ae8270604c41fd1e7f2c0f00bd2b3ba3cd87f6/spoon.Rcheck/00check.log for details. =============================== BiocCheck('spoon_0.99.7.tar.gz') =============================== BiocCheckVersion: 1.39.26 BiocVersion: 3.19 Package: spoon PackageVersion: 0.99.7 sourceDir: /tmp/RtmpoEuJBO/file2ca16245a5626f/spoon installDir: /tmp/RtmpoEuJBO/file2ca16222373ae6 BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3278/a4ae8270604c41fd1e7f2c0f00bd2b3ba3cd87f6/spoon.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... * 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... * Checking for recommended DESCRIPTION fields... * Checking for Bioconductor software dependencies... Bioconductor dependencies found in Imports & Depends (50%). * Checking for pinned package versions in DESCRIPTION... * 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 spoon... * Checking coding practice... * NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions * Checking parsed R code in R directory, examples, vignettes... * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times) * Checking function lengths... * NOTE: The recommended function length is 50 lines or less. There are 2 functions greater than 50 lines. * Checking man page documentation... * Checking package NEWS... * 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; 8 lines (1%) are > 80 characters long. * NOTE: Consider multiples of 4 spaces for line indents; 206 lines (23%) 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 is in the Support Site Watched Tags. BiocCheck results 0 ERRORS | 0 WARNINGS | 5 NOTES See the spoon.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details.
nebbiolo1 BUILD BIN output
merida1 Summary
Package: spoon |
Version: 0.99.7 |
RVersion: 4.4 |
BiocVersion: 3.19 |
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data spoon |
BuildTime: 4 minutes 20.85 seconds |
CheckCommand: BiocCheckGitClone('spoon') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3278/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3278/a4ae8270604c41fd1e7f2c0f00bd2b3ba3cd87f6/spoon.install-out.txt spoon_0.99.7.tar.gz && BiocCheck('spoon_0.99.7.tar.gz', `new-package`=TRUE) |
CheckTime: 9 minutes 34.69 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh spoon_0.99.7.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 27.34 seconds |
PackageFileSize: 813.45 KiB |
BuildID:: spoon_20240221195521 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: spoon. 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. Adding Build Product Information to Database.Checking Package status: 0. Build Package status: 0. |
merida1 BUILD SRC output
=============================== R CMD BUILD =============================== * checking for file spoon/DESCRIPTION ... OK * preparing spoon: * 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 spoon_0.99.7.tar.gz
merida1 CHECK output
=============================== BiocCheckGitClone('spoon') =============================== BiocCheckVersion: 1.39.26 BiocVersion: 3.19 Package: spoon PackageVersion: 0.99.7 sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3278/a4ae8270604c41fd1e7f2c0f00bd2b3ba3cd87f6/spoon 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... * NOTE: (Optional) CITATION file not found. Only include a CITATION file if there is a preprint or publication for this Bioconductor package. Note that Bioconductor packages are not required to have a CITATION file but it is useful both for users and for tracking Bioconductor project-wide metrics. When including a CITATION file, add the publication using the 'doi' argument of 'bibentry()'. BiocCheck results 0 ERRORS | 0 WARNINGS | 1 NOTES For more details, run browseVignettes(package = 'BiocCheck') =============================== R CMD CHECK =============================== * using log directory /Users/pkgbuild/packagebuilder/workers/jobs/3278/a4ae8270604c41fd1e7f2c0f00bd2b3ba3cd87f6/spoon.Rcheck * using R Under development (unstable) (2024-01-16 r85808) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option --no-vignettes * checking for file spoon/DESCRIPTION ... OK * this is package spoon version 0.99.7 * 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 spoon 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 ... NOTE License stub is invalid DCF. * 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 ... [17s/19s] OK * checking whether the package can be loaded with stated dependencies ... [17s/18s] OK * checking whether the package can be unloaded cleanly ... [16s/17s] OK * checking whether the namespace can be loaded with stated dependencies ... [15s/16s] OK * checking whether the namespace can be unloaded cleanly ... [14s/16s] OK * checking loading without being on the library search path ... [14s/16s] OK * checking use of S3 registration ... 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 ... [29s/29s] 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 ... [169s/176s] OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed weighted_nnSVG 108.149 3.887 112.161 generate_weights 43.670 2.655 53.018 * checking for unstated dependencies in tests ... OK * checking tests ... Running testthat.R [125s/132s] [125s/132s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... [6s/6s] OK * DONE Status: 1 NOTE See /Users/pkgbuild/packagebuilder/workers/jobs/3278/a4ae8270604c41fd1e7f2c0f00bd2b3ba3cd87f6/spoon.Rcheck/00check.log for details. =============================== BiocCheck('spoon_0.99.7.tar.gz') =============================== BiocCheckVersion: 1.39.26 BiocVersion: 3.19 Package: spoon PackageVersion: 0.99.7 sourceDir: /var/folders/97/7zyjn3nj10x926_ht39w_4lm0000gt/T//RtmpYm4DPC/file1ee34da91a64/spoon installDir: /var/folders/97/7zyjn3nj10x926_ht39w_4lm0000gt/T//RtmpYm4DPC/file1ee345fb9deb BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3278/a4ae8270604c41fd1e7f2c0f00bd2b3ba3cd87f6/spoon.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... * 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... * Checking for recommended DESCRIPTION fields... * Checking for Bioconductor software dependencies... Bioconductor dependencies found in Imports & Depends (50%). * Checking for pinned package versions in DESCRIPTION... * 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 spoon... * Checking coding practice... * NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions * Checking parsed R code in R directory, examples, vignettes... * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times) * Checking function lengths... * NOTE: The recommended function length is 50 lines or less. There are 2 functions greater than 50 lines. * Checking man page documentation... * Checking package NEWS... * 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; 8 lines (1%) are > 80 characters long. * NOTE: Consider multiples of 4 spaces for line indents; 206 lines (23%) 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 is in the Support Site Watched Tags. BiocCheck results 0 ERRORS | 0 WARNINGS | 5 NOTES See the spoon.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details.
merida1 BUILD BIN output
=============================== R CMD BUILD =============================== >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir spoon_0.99.7.tar.gz' >>>>>>> * installing *source* package spoon ... ** using staged installation ** R ** 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 (spoon)