Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:58 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the BiocCheck package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocCheck.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. |
Package 159/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BiocCheck 1.28.0 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: BiocCheck |
Version: 1.28.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocCheck.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BiocCheck_1.28.0.tar.gz |
StartedAt: 2021-10-14 20:09:13 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 20:16:27 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 434.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BiocCheck.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocCheck.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BiocCheck_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BiocCheck.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'BiocCheck/DESCRIPTION' ... OK * this is package 'BiocCheck' version '1.28.0' * checking package namespace information ... OK * checking package dependencies ... NOTE Package which this enhances but not available for checking: 'codetoolsBioC' * 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 whether package 'BiocCheck' 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 Unexported objects imported by ':::' calls: 'BiocManager:::.version_bioc' 'knitr:::detect_pattern' 'tools:::.build_news_db_from_package_NEWS_Rd' 'tools:::.build_news_db_from_package_NEWS_md' 'tools:::.news_reader_default' 'tools:::RdTags' 'tools:::str_parse_logic' 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 ... 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed BiocCheck 24.2 0.34 29.6 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed BiocCheck 21.14 0.41 26.52 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' OK ** running tests for arch 'x64' ... Running 'runTests.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: 2 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BiocCheck.Rcheck/00check.log' for details.
BiocCheck.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/BiocCheck_1.28.0.tar.gz && rm -rf BiocCheck.buildbin-libdir && mkdir BiocCheck.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocCheck.buildbin-libdir BiocCheck_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL BiocCheck_1.28.0.zip && rm BiocCheck_1.28.0.tar.gz BiocCheck_1.28.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 7 4020k 7 303k 0 0 771k 0 0:00:05 --:--:-- 0:00:05 771k 73 4020k 73 2958k 0 0 2117k 0 0:00:01 0:00:01 --:--:-- 2117k 100 4020k 100 4020k 0 0 2348k 0 0:00:01 0:00:01 --:--:-- 2348k install for i386 * installing *source* package 'BiocCheck' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'BiocCheck' finding HTML links ... done BiocCheck html BiocCheckGitClone html ** 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 install for x64 * installing *source* package 'BiocCheck' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'BiocCheck' as BiocCheck_1.28.0.zip * DONE (BiocCheck) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'BiocCheck' successfully unpacked and MD5 sums checked
BiocCheck.Rcheck/tests_i386/runTests.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-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. > BiocGenerics:::testPackage("BiocCheck") Loading required package: usethis * NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed * ERROR: System Files found that should not be git tracked: something.Rproj * Checking for blank lines in DESCRIPTION... * Checking if DESCRIPTION is well formatted... * Checking for proper Description: field... * Checking for whitespace in DESCRIPTION field names... * ERROR: Remove whitespace from DESCRIPTION field names. * Checking for blank lines in DESCRIPTION... * ERROR: Remove blank lines from DESCRIPTION. * WARNING: Description field in the DESCRIPTION file is too concise * NOTE: The Description field in the DESCRIPTION is made up by less than 3 sentences. Please consider expanding this field, and structure it as a full paragraph * 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... * ERROR: Package directory 'unitTestTempDir' must match Package: field (got 'Foo'). * 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... * ERROR: No 'Version:' field in DESCRIPTION. * 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... * ERROR: Authors@R must evaluate to 'person' object. * 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... * ERROR: Authors@R field in DESCRIPTION file is malformed. * 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... * ERROR: Package directory 'unitTestTempDir' must match Package: field (got ''). * 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... * ERROR: Do not use Author/Maintainer fields. Use Authors@R. * ERROR: Remove Maintainer field. Use Authors@R [cre] designation. * Checking if DESCRIPTION is well formatted... * Checking for valid maintainer... * ERROR: Use Authors@R field not Author/Maintainer fields. Do not use both. * 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... * NOTE: Invalid ORCID ID for Bioconductor Package Maintainer * 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... * ERROR: Do not use Author/Maintainer fields. Use Authors@R. * ERROR: Remove Maintainer field. Use Authors@R [cre] designation. * 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... * ERROR: Designated only one maintainer with Authors@R [cre]. * 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 that provided CITATION file is correctly formatted... * Checking that provided CITATION file is correctly formatted... * NOTE: CITATION file might be not correctly formatted * Checking that biocViews are present... * ERROR: No biocViews terms found. * 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... * WARNING: 'foo' is an invalid BiocViews term. * WARNING: 'Cancer' is an invalid BiocViews term. * WARNING: 'bar' is an invalid BiocViews term. Did you mean: 'ag' * WARNING: 'baz' is an invalid BiocViews term. Did you mean: 'ag' * Checking for recommended 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 that biocViews are present... * Checking package type based on biocViews... Software * Checking for non-trivial biocViews... * Checking that biocViews come from the same category... * WARNING: Use biocViews from one category only (one of Software, ExperimentData, AnnotationData, Workflow) * ERROR: Use 'BiocParallel' instead of 'multicore'. 'multicore' is deprecated and does not work on Windows. * ERROR: At least 80% of man pages documenting exported objects must have runnable examples. The following pages do not: baddep.Rd * NOTE: Usage of dontrun{} / donttest{} found in man page examples. 67% of man pages use one of these cases. Found in the following files: a.Rd baddep.Rd * NOTE: Use donttest{} instead of dontrun{}. Found in the following files: baddep.Rd * Checking if other packages can import this one... * ERROR: Packages providing 1 object(s) used in this package should be imported in the NAMESPACE file, otherwise packages importing this package may fail. package::object in function() RJSONIO::isValidJSON in baddep() * Checking to see if we understand object initialization... * NOTE: Consider clarifying how 5 object(s) are initialized. Maybe they are part of a data set loaded with data(), or perhaps part of an object referenced in with() or within(). function (object) bad_dl (download.file) bad_fun (update.packages) has_devel (R) iambad (colone) invalid_ref (BiocCheck) Found browser() in R/morecode.R (line 1, column 12) Found @ in * NOTE: Use accessors; don't access S4 class slots via '@' in examples/vignettes. * NOTE: Remove generated comments from man pages a.Rd, baddep.Rd Maintainer is registered at support site. * ERROR: Maintainer must register at the support site; visit https://support.bioconductor.org/accounts/signup/ . Maintainer is registered at support site. Package name is in support site watched tags. * ERROR: Maintainer must add package name to Watched Tags on the support site; Edit your Support Site User Profile to add Watched Tags. Package name is in support site watched tags. Package name is in support site watched tags. * ERROR: Version number in tarball filename must match Version field in DESCRIPTION. (Tip: create tarball with R CMD build) * NOTE: Consider shorter lines; 1 lines (0%) are > 80 characters long. First 1 lines: R/morebadcode.R:2 # this is a really long line with many characters in ... * NOTE: Consider 4 spaces instead of tabs; 2 lines (1%) contain tabs. First 2 lines: man/a.Rd:48 ##-- or do help(data=index) for the standard data sets. man/baddep.Rd:41 ##-- or do help(data=index) for the standard data sets. * NOTE: Consider multiples of 4 spaces for line indents, 1 lines(0%) are not. First 1 lines: R/morebadcode.R:6 # something other than a multiple of 5 spaces! See http://bioconductor.org/developers/how-to/coding-style/ See styler package: https://cran.r-project.org/package=styler as described in the BiocCheck vignette. * Checking License: for restrictive use... * Checking License: for restrictive use... * ERROR: License 'CC BY-NC-ND 4.0' restricts use * Checking License: for restrictive use... * ERROR: License 'CC BY-NC-ND 4.0 + file LICENSE' restricts use * Checking License: for restrictive use... * NOTE: License 'UNKNOWN' unknown; licenses cannot restrict use * Checking License: for restrictive use... * NOTE: malformed 'License:' field 'NA' * NOTE: Consider adding a NEWS file, so your package news will be included in Bioconductor release announcements. * WARNING: Fix formatting of NEWS.Rd. Malformed package NEWS will not be included in Bioconductor release announcements. * NOTE: More than 1 NEWS file found. See ?news for recognition ordering. Please remove one of the following: C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpMDyj81/unitTestTempDir/inst/NEWS.Rd C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpMDyj81/unitTestTempDir/./NEWS.md * WARNING: Fix formatting of NEWS.Rd. Malformed package NEWS will not be included in Bioconductor release announcements. * WARNING: New package x version starting with non-zero value (e.g., 1.y.z, 2.y.z); got '1.99.3'. * ERROR: New package y version not 99 (e.g., x.99.z, x.99.z, ...); got '0.2.3'. * NOTE: Update R version dependency from 1.0.0 to 4.1. * NOTE: Consider adding unit tests. We strongly encourage them. See http://bioconductor.org/developers/how-to/unitTesting-guidelines/. * NOTE: skip_on_bioc() found in testthat files: a_test.R * NOTE: install, biocLite, install.packages, or update.packages found in R files bad_coding.R: 3 * ERROR: Invalid package Version, see http://www.bioconductor.org/developers/how-to/version-numbering/ * ERROR: Invalid package Version, see http://www.bioconductor.org/developers/how-to/version-numbering/ * WARNING: y of x.y.z version should be even in release * NOTE: Update R version dependency from 4.0 to 4.1. * ERROR: Package must be removed from CRAN. * ERROR: 'GenomicRanges' already exists in Bioconductor. * ERROR: 'GO.db' already exists in Bioconductor. * ERROR: 'TENxBrainData' already exists in Bioconductor. * ERROR: 'annotation' already exists in Bioconductor. * ERROR: Package dependencies must be on CRAN or Bioconductor. Remove 'Remotes:' from DESCRIPTION * ERROR: No 'vignettes' directory. * ERROR: No vignette sources in vignettes/ directory. * WARNING: Vignette[s] missing '\%VignetteIndexEntry{Vignette Title}'. Update the following files: test.Rnw * WARNING: Remove vignette sources from inst/doc; they belong in vignettes/. * WARNING: Remove vignette sources from inst/doc; they belong in vignettes/. * ERROR: VignetteBuilder listed in DESCRIPTION but not found as VignetteEngine in any vignettes: knitr * WARNING: Package listed as VignetteEngine or VignetteBuilder but not currently Suggested. Add the following to Suggests in DESCRIPTION: knitr * WARNING: Package listed as VignetteEngine or VignetteBuilder but not currently Suggested. Add the following to Suggests in DESCRIPTION: Sweave * ERROR: VignetteBuilder listed in DESCRIPTION but not found as VignetteEngine in any vignettes: knitr * WARNING: Vignette[s] missing Vignette metadata. See http://r-pkgs.had.co.nz/vignettes.html ; Update the following files: testpkg0.Rmd testpkg0_child.Rmd * ERROR: No VignetteEngine specified in vignette or DESCRIPTION. Add VignetteEngine to the following files or add a default VignetteBuilder in DESCRIPTION: testpkg0.Rmd testpkg0_child.Rmd * WARNING: Package listed as VignetteEngine or VignetteBuilder but not currently Suggested. Add the following to Suggests in DESCRIPTION: knitr * WARNING: Vignette[s] still using 'VignetteIndexEntry{Vignette Title}' Update the following files from using template values: testpkg0.Rmd * WARNING: Vignette[s] missing '\%VignetteIndexEntry{Vignette Title}'. Update the following files: testpkg0_child.Rmd * WARNING: Evaluate more vignette chunks. # of code chunks: 6 # of eval=FALSE: 3 # of nonexecutable code chunks by syntax: 0 # total unevaluated 3 (50%) * NOTE: Potential intermediate files found: vignettes/testpkg0.html * ERROR: VignetteBuilder listed in DESCRIPTION but not found as VignetteEngine in any vignettes: FailBuilder * WARNING: Vignette[s] missing Vignette metadata. See http://r-pkgs.had.co.nz/vignettes.html ; Update the following files: testpkg0.Rmd * ERROR: VignetteEngine specified but not in DESCRIPTION. Add the VignetteEngine from the following files to DESCRIPTION: testpkg0.Rmd * WARNING: Package listed as VignetteEngine or VignetteBuilder but not currently Suggested. Add the following to Suggests in DESCRIPTION: ThisWillFail FailBuilder * WARNING: Evaluate more vignette chunks. # of code chunks: 2 # of eval=FALSE: 0 # of nonexecutable code chunks by syntax: 1 # total unevaluated 1 (50%) * NOTE: Potential intermediate files found: vignettes/testpkg0.html RUNIT TEST PROTOCOL -- Thu Oct 14 20:13:53 2021 *********************************************** Number of test functions: 39 Number of errors: 0 Number of failures: 0 1 Test Suite : BiocCheck RUnit Tests - 39 test functions, 0 errors, 0 failures Number of test functions: 39 Number of errors: 0 Number of failures: 0 Warning messages: 1: In sprintf("Package: ", UNIT_TEST_PKG) : one argument not used by format 'Package: ' 2: In sprintf("Depends: multicore", UNIT_TEST_PKG) : one argument not used by format 'Depends: multicore' > > proc.time() user system elapsed 111.17 15.26 159.15 |
BiocCheck.Rcheck/tests_x64/runTests.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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. > BiocGenerics:::testPackage("BiocCheck") Loading required package: usethis * NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed * ERROR: System Files found that should not be git tracked: something.Rproj * Checking for blank lines in DESCRIPTION... * Checking if DESCRIPTION is well formatted... * Checking for proper Description: field... * Checking for whitespace in DESCRIPTION field names... * ERROR: Remove whitespace from DESCRIPTION field names. * Checking for blank lines in DESCRIPTION... * ERROR: Remove blank lines from DESCRIPTION. * WARNING: Description field in the DESCRIPTION file is too concise * NOTE: The Description field in the DESCRIPTION is made up by less than 3 sentences. Please consider expanding this field, and structure it as a full paragraph * 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... * ERROR: Package directory 'unitTestTempDir' must match Package: field (got 'Foo'). * 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... * ERROR: No 'Version:' field in DESCRIPTION. * 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... * ERROR: Authors@R must evaluate to 'person' object. * 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... * ERROR: Authors@R field in DESCRIPTION file is malformed. * 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... * ERROR: Package directory 'unitTestTempDir' must match Package: field (got ''). * 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... * ERROR: Do not use Author/Maintainer fields. Use Authors@R. * ERROR: Remove Maintainer field. Use Authors@R [cre] designation. * Checking if DESCRIPTION is well formatted... * Checking for valid maintainer... * ERROR: Use Authors@R field not Author/Maintainer fields. Do not use both. * 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... * NOTE: Invalid ORCID ID for Bioconductor Package Maintainer * 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... * ERROR: Do not use Author/Maintainer fields. Use Authors@R. * ERROR: Remove Maintainer field. Use Authors@R [cre] designation. * 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... * ERROR: Designated only one maintainer with Authors@R [cre]. * 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 that provided CITATION file is correctly formatted... * Checking that provided CITATION file is correctly formatted... * NOTE: CITATION file might be not correctly formatted * Checking that biocViews are present... * ERROR: No biocViews terms found. * 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... * WARNING: 'foo' is an invalid BiocViews term. * WARNING: 'Cancer' is an invalid BiocViews term. * WARNING: 'bar' is an invalid BiocViews term. Did you mean: 'ag' * WARNING: 'baz' is an invalid BiocViews term. Did you mean: 'ag' * Checking for recommended 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 that biocViews are present... * Checking package type based on biocViews... Software * Checking for non-trivial biocViews... * Checking that biocViews come from the same category... * WARNING: Use biocViews from one category only (one of Software, ExperimentData, AnnotationData, Workflow) * ERROR: Use 'BiocParallel' instead of 'multicore'. 'multicore' is deprecated and does not work on Windows. * ERROR: At least 80% of man pages documenting exported objects must have runnable examples. The following pages do not: baddep.Rd * NOTE: Usage of dontrun{} / donttest{} found in man page examples. 67% of man pages use one of these cases. Found in the following files: a.Rd baddep.Rd * NOTE: Use donttest{} instead of dontrun{}. Found in the following files: baddep.Rd * Checking if other packages can import this one... * ERROR: Packages providing 1 object(s) used in this package should be imported in the NAMESPACE file, otherwise packages importing this package may fail. package::object in function() RJSONIO::isValidJSON in baddep() * Checking to see if we understand object initialization... * NOTE: Consider clarifying how 5 object(s) are initialized. Maybe they are part of a data set loaded with data(), or perhaps part of an object referenced in with() or within(). function (object) bad_dl (download.file) bad_fun (update.packages) has_devel (R) iambad (colone) invalid_ref (BiocCheck) Found browser() in R/morecode.R (line 1, column 12) Found @ in * NOTE: Use accessors; don't access S4 class slots via '@' in examples/vignettes. * NOTE: Remove generated comments from man pages a.Rd, baddep.Rd Maintainer is registered at support site. * ERROR: Maintainer must register at the support site; visit https://support.bioconductor.org/accounts/signup/ . Maintainer is registered at support site. Package name is in support site watched tags. * ERROR: Maintainer must add package name to Watched Tags on the support site; Edit your Support Site User Profile to add Watched Tags. Package name is in support site watched tags. Package name is in support site watched tags. * ERROR: Version number in tarball filename must match Version field in DESCRIPTION. (Tip: create tarball with R CMD build) * NOTE: Consider shorter lines; 1 lines (0%) are > 80 characters long. First 1 lines: R/morebadcode.R:2 # this is a really long line with many characters in ... * NOTE: Consider 4 spaces instead of tabs; 2 lines (1%) contain tabs. First 2 lines: man/a.Rd:48 ##-- or do help(data=index) for the standard data sets. man/baddep.Rd:41 ##-- or do help(data=index) for the standard data sets. * NOTE: Consider multiples of 4 spaces for line indents, 1 lines(0%) are not. First 1 lines: R/morebadcode.R:6 # something other than a multiple of 5 spaces! See http://bioconductor.org/developers/how-to/coding-style/ See styler package: https://cran.r-project.org/package=styler as described in the BiocCheck vignette. * Checking License: for restrictive use... * Checking License: for restrictive use... * ERROR: License 'CC BY-NC-ND 4.0' restricts use * Checking License: for restrictive use... * ERROR: License 'CC BY-NC-ND 4.0 + file LICENSE' restricts use * Checking License: for restrictive use... * NOTE: License 'UNKNOWN' unknown; licenses cannot restrict use * Checking License: for restrictive use... * NOTE: malformed 'License:' field 'NA' * NOTE: Consider adding a NEWS file, so your package news will be included in Bioconductor release announcements. * WARNING: Fix formatting of NEWS.Rd. Malformed package NEWS will not be included in Bioconductor release announcements. * NOTE: More than 1 NEWS file found. See ?news for recognition ordering. Please remove one of the following: C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpyUZZZH/unitTestTempDir/inst/NEWS.Rd C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpyUZZZH/unitTestTempDir/./NEWS.md * WARNING: Fix formatting of NEWS.Rd. Malformed package NEWS will not be included in Bioconductor release announcements. * WARNING: New package x version starting with non-zero value (e.g., 1.y.z, 2.y.z); got '1.99.3'. * ERROR: New package y version not 99 (e.g., x.99.z, x.99.z, ...); got '0.2.3'. * NOTE: Update R version dependency from 1.0.0 to 4.1. * NOTE: Consider adding unit tests. We strongly encourage them. See http://bioconductor.org/developers/how-to/unitTesting-guidelines/. * NOTE: skip_on_bioc() found in testthat files: a_test.R * NOTE: install, biocLite, install.packages, or update.packages found in R files bad_coding.R: 3 * ERROR: Invalid package Version, see http://www.bioconductor.org/developers/how-to/version-numbering/ * ERROR: Invalid package Version, see http://www.bioconductor.org/developers/how-to/version-numbering/ * WARNING: y of x.y.z version should be even in release * NOTE: Update R version dependency from 4.0 to 4.1. * ERROR: Package must be removed from CRAN. * ERROR: 'GenomicRanges' already exists in Bioconductor. * ERROR: 'GO.db' already exists in Bioconductor. * ERROR: 'TENxBrainData' already exists in Bioconductor. * ERROR: 'annotation' already exists in Bioconductor. * ERROR: Package dependencies must be on CRAN or Bioconductor. Remove 'Remotes:' from DESCRIPTION * ERROR: No 'vignettes' directory. * ERROR: No vignette sources in vignettes/ directory. * WARNING: Vignette[s] missing '\%VignetteIndexEntry{Vignette Title}'. Update the following files: test.Rnw * WARNING: Remove vignette sources from inst/doc; they belong in vignettes/. * WARNING: Remove vignette sources from inst/doc; they belong in vignettes/. * ERROR: VignetteBuilder listed in DESCRIPTION but not found as VignetteEngine in any vignettes: knitr * WARNING: Package listed as VignetteEngine or VignetteBuilder but not currently Suggested. Add the following to Suggests in DESCRIPTION: knitr * WARNING: Package listed as VignetteEngine or VignetteBuilder but not currently Suggested. Add the following to Suggests in DESCRIPTION: Sweave * ERROR: VignetteBuilder listed in DESCRIPTION but not found as VignetteEngine in any vignettes: knitr * WARNING: Vignette[s] missing Vignette metadata. See http://r-pkgs.had.co.nz/vignettes.html ; Update the following files: testpkg0.Rmd testpkg0_child.Rmd * ERROR: No VignetteEngine specified in vignette or DESCRIPTION. Add VignetteEngine to the following files or add a default VignetteBuilder in DESCRIPTION: testpkg0.Rmd testpkg0_child.Rmd * WARNING: Package listed as VignetteEngine or VignetteBuilder but not currently Suggested. Add the following to Suggests in DESCRIPTION: knitr * WARNING: Vignette[s] still using 'VignetteIndexEntry{Vignette Title}' Update the following files from using template values: testpkg0.Rmd * WARNING: Vignette[s] missing '\%VignetteIndexEntry{Vignette Title}'. Update the following files: testpkg0_child.Rmd * WARNING: Evaluate more vignette chunks. # of code chunks: 6 # of eval=FALSE: 3 # of nonexecutable code chunks by syntax: 0 # total unevaluated 3 (50%) * NOTE: Potential intermediate files found: vignettes/testpkg0.html * ERROR: VignetteBuilder listed in DESCRIPTION but not found as VignetteEngine in any vignettes: FailBuilder * WARNING: Vignette[s] missing Vignette metadata. See http://r-pkgs.had.co.nz/vignettes.html ; Update the following files: testpkg0.Rmd * ERROR: VignetteEngine specified but not in DESCRIPTION. Add the VignetteEngine from the following files to DESCRIPTION: testpkg0.Rmd * WARNING: Package listed as VignetteEngine or VignetteBuilder but not currently Suggested. Add the following to Suggests in DESCRIPTION: ThisWillFail FailBuilder * WARNING: Evaluate more vignette chunks. # of code chunks: 2 # of eval=FALSE: 0 # of nonexecutable code chunks by syntax: 1 # total unevaluated 1 (50%) * NOTE: Potential intermediate files found: vignettes/testpkg0.html RUNIT TEST PROTOCOL -- Thu Oct 14 20:16:09 2021 *********************************************** Number of test functions: 39 Number of errors: 0 Number of failures: 0 1 Test Suite : BiocCheck RUnit Tests - 39 test functions, 0 errors, 0 failures Number of test functions: 39 Number of errors: 0 Number of failures: 0 Warning messages: 1: In sprintf("Package: ", UNIT_TEST_PKG) : one argument not used by format 'Package: ' 2: In sprintf("Depends: multicore", UNIT_TEST_PKG) : one argument not used by format 'Depends: multicore' > > proc.time() user system elapsed 85.45 24.57 135.03 |
BiocCheck.Rcheck/examples_i386/BiocCheck-Ex.timings
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BiocCheck.Rcheck/examples_x64/BiocCheck-Ex.timings
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