Bioconductor Single Package Builder - Build History
nebbiolo2 Summary
Package: dreamlet |
Version: 0.99.20 |
RVersion: 4.3 |
BiocVersion: 3.18 |
BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data dreamlet |
BuildTime: 6 minutes 33.47 seconds |
CheckCommand: BiocCheckGitClone('dreamlet') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2955/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2955/4d4000c52bd5c269e2f768bf1f669800ac3c7a1d/dreamlet.install-out.txt dreamlet_0.99.20.tar.gz && BiocCheck('dreamlet_0.99.20.tar.gz', `new-package`=TRUE) |
CheckTime: 8 minutes 38.64 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 3443.29 KiB |
BuildID:: dreamlet_20230703163838 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: dreamlet. 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: 0. |
nebbiolo2 BUILD SRC output
=============================== R CMD BUILD =============================== * checking for file ‘dreamlet/DESCRIPTION’ ... OK * preparing ‘dreamlet’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to process help pages Loading required namespace: dreamlet * saving partial Rd database * creating vignettes ... OK * cleaning src * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘dreamlet_0.99.20.tar.gz’
nebbiolo2 CHECK output
=============================== BiocCheckGitClone('dreamlet') =============================== ─ BiocCheckVersion: 1.37.4 ─ BiocVersion: 3.18 ─ Package: dreamlet ─ PackageVersion: 0.99.20 ─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2955/4d4000c52bd5c269e2f768bf1f669800ac3c7a1d/dreamlet ─ 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... * Checking that provided CITATION file is correctly formatted... ─ 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/2955/4d4000c52bd5c269e2f768bf1f669800ac3c7a1d/dreamlet.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 * running under: Ubuntu 22.04.2 LTS * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘dreamlet/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘dreamlet’ version ‘0.99.20’ * 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 ‘dreamlet’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * 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 ... [11s/11s] OK * checking whether the package can be loaded with stated dependencies ... [11s/11s] OK * checking whether the package can be unloaded cleanly ... [11s/11s] OK * checking whether the namespace can be loaded with stated dependencies ... [11s/11s] OK * checking whether the namespace can be unloaded cleanly ... [11s/11s] OK * checking loading without being on the library search path ... [11s/11s] 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 ... [40s/40s] OK * checking Rd files ... [11s/11s] 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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... [214s/214s] OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed zenith_gsa-methods 51.503 1.544 53.049 fitVarPart 15.433 0.112 15.545 plotVarPart-methods 15.017 0.032 15.050 sortCols-method 14.918 0.024 14.942 plotPercentBars-methods 14.789 0.084 14.873 run_mash 8.922 0.020 8.944 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ [39s/51s] [39s/51s] 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: 2 NOTEs See ‘/home/pkgbuild/packagebuilder/workers/jobs/2955/4d4000c52bd5c269e2f768bf1f669800ac3c7a1d/dreamlet.Rcheck/00check.log’ for details. =============================== BiocCheck('dreamlet_0.99.20.tar.gz') =============================== ─ BiocCheckVersion: 1.37.4 ─ BiocVersion: 3.18 ─ Package: dreamlet ─ PackageVersion: 0.99.20 ─ sourceDir: /tmp/Rtmp4d2hOX/file1d8b286263427a/dreamlet ─ installDir: /tmp/Rtmp4d2hOX/file1d8b28ea0dc1a ─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2955/4d4000c52bd5c269e2f768bf1f669800ac3c7a1d/dreamlet.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: Microarray 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... * Checking for pinned package versions... * Checking DESCRIPTION/NAMESPACE consistency... * Checking .Rbuildignore... * Checking for stray BiocCheck output folders... * Checking vignette directory... * NOTE: 'sessionInfo' not found in vignette(s) * Checking whether vignette is built with 'R CMD build'... * Checking package installation calls in R code... Warning in tools::parse_Rd(infile) : /tmp/Rtmp4d2hOX/file1d8b286263427a/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite' Warning in tools::parse_Rd(infile) : /tmp/Rtmp4d2hOX/file1d8b286263427a/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite' Warning in tools::parse_Rd(infile) : /tmp/Rtmp4d2hOX/file1d8b286263427a/dreamlet/man/run_mash.Rd:103: unknown macro '\insertAllCited' Warning in tools::parse_Rd(infile) : /tmp/Rtmp4d2hOX/file1d8b286263427a/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite' Warning in tools::parse_Rd(infile) : /tmp/Rtmp4d2hOX/file1d8b286263427a/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite' * Checking for library/require of dreamlet... * Checking coding practice... * NOTE: Avoid 1:...; use seq_len() or seq_along() * NOTE: Avoid using '=' for assignment and use '<-' instead * Checking parsed R code in R directory, examples, vignettes... * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times) * Checking function lengths... * NOTE: The recommended function length is 50 lines or less. There are 18 functions greater than 50 lines. * Checking man page documentation... Warning in tools::parse_Rd(manpage) : /tmp/Rtmp4d2hOX/file1d8b286263427a/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite' Warning in tools::parse_Rd(manpage) : /tmp/Rtmp4d2hOX/file1d8b286263427a/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite' Warning in tools::parse_Rd(manpage) : /tmp/Rtmp4d2hOX/file1d8b286263427a/dreamlet/man/run_mash.Rd:103: unknown macro '\insertAllCited' Warning in tools::parse_Rd(manpage) : /tmp/Rtmp4d2hOX/file1d8b286263427a/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite' Warning in tools::parse_Rd(manpage) : /tmp/Rtmp4d2hOX/file1d8b286263427a/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite' * WARNING: Empty or missing \value sections found in man pages. Warning in tools::parse_Rd(manpage) : /tmp/Rtmp4d2hOX/file1d8b286263427a/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite' Warning in tools::parse_Rd(manpage) : /tmp/Rtmp4d2hOX/file1d8b286263427a/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite' Warning in tools::parse_Rd(manpage) : /tmp/Rtmp4d2hOX/file1d8b286263427a/dreamlet/man/run_mash.Rd:103: unknown macro '\insertAllCited' Warning in tools::parse_Rd(manpage) : /tmp/Rtmp4d2hOX/file1d8b286263427a/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite' Warning in tools::parse_Rd(manpage) : /tmp/Rtmp4d2hOX/file1d8b286263427a/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite' Warning in tools::parse_Rd(manpage) : /tmp/Rtmp4d2hOX/file1d8b286263427a/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite' Warning in tools::parse_Rd(manpage) : /tmp/Rtmp4d2hOX/file1d8b286263427a/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite' Warning in tools::parse_Rd(manpage) : /tmp/Rtmp4d2hOX/file1d8b286263427a/dreamlet/man/run_mash.Rd:103: unknown macro '\insertAllCited' Warning in tools::parse_Rd(manpage) : /tmp/Rtmp4d2hOX/file1d8b286263427a/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite' Warning in tools::parse_Rd(manpage) : /tmp/Rtmp4d2hOX/file1d8b286263427a/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite' * 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; 407 lines (4%) are > 80 characters long. * NOTE: Consider 4 spaces instead of tabs; 1903 lines (19%) contain tabs. * NOTE: Consider multiples of 4 spaces for line indents; 518 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 ── 0 ERRORS | 1 WARNINGS | 9 NOTES See the dreamlet.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details.
nebbiolo2 BUILD BIN output
lconway Summary
Package: dreamlet |
Version: 0.99.20 |
RVersion: 4.3 |
BiocVersion: 3.18 |
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data dreamlet |
BuildTime: 4 minutes 41.10 seconds |
CheckCommand: BiocCheckGitClone('dreamlet') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/2955/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/2955/4d4000c52bd5c269e2f768bf1f669800ac3c7a1d/dreamlet.install-out.txt dreamlet_0.99.20.tar.gz && BiocCheck('dreamlet_0.99.20.tar.gz', `new-package`=TRUE) |
CheckTime: 6 minutes 18.83 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh dreamlet_0.99.20.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 36.09 seconds |
PackageFileSize: 3603.93 KiB |
BuildID:: dreamlet_20230703163838 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: dreamlet. 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: 0. Build Package status: 0. |
lconway BUILD SRC output
=============================== R CMD BUILD =============================== * checking for file ‘dreamlet/DESCRIPTION’ ... OK * preparing ‘dreamlet’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to process help pages Loading required namespace: dreamlet * saving partial Rd database * creating vignettes ... OK * cleaning src * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘dreamlet_0.99.20.tar.gz’
lconway CHECK output
=============================== BiocCheckGitClone('dreamlet') =============================== ─ BiocCheckVersion: 1.37.4 ─ BiocVersion: 3.18 ─ Package: dreamlet ─ PackageVersion: 0.99.20 ─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2955/4d4000c52bd5c269e2f768bf1f669800ac3c7a1d/dreamlet ─ 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... * Checking that provided CITATION file is correctly formatted... ─ 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/2955/4d4000c52bd5c269e2f768bf1f669800ac3c7a1d/dreamlet.Rcheck’ * using R version 4.3.1 Patched (2023-06-17 r84564) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘dreamlet/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘dreamlet’ version ‘0.99.20’ * 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 ‘dreamlet’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * 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 ... [8s/8s] OK * checking whether the package can be loaded with stated dependencies ... [8s/8s] OK * checking whether the package can be unloaded cleanly ... [8s/8s] OK * checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK * checking whether the namespace can be unloaded cleanly ... [8s/8s] OK * checking loading without being on the library search path ... [8s/8s] 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 ... [28s/29s] OK * checking Rd files ... [8s/8s] 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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... [152s/152s] OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed zenith_gsa-methods 37.286 2.627 39.946 fitVarPart 10.123 0.095 10.218 plotVarPart-methods 9.871 0.046 9.917 sortCols-method 9.823 0.057 9.881 plotPercentBars-methods 9.688 0.055 9.744 run_mash 6.490 0.169 6.666 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ [28s/37s] [28s/37s] 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 ... [6s/6s] OK * DONE Status: 2 NOTEs See ‘/Users/pkgbuild/packagebuilder/workers/jobs/2955/4d4000c52bd5c269e2f768bf1f669800ac3c7a1d/dreamlet.Rcheck/00check.log’ for details. =============================== BiocCheck('dreamlet_0.99.20.tar.gz') =============================== ─ BiocCheckVersion: 1.37.4 ─ BiocVersion: 3.18 ─ Package: dreamlet ─ PackageVersion: 0.99.20 ─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmptpHVA7/file14eb06492de24/dreamlet ─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmptpHVA7/file14eb073e9f783 ─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2955/4d4000c52bd5c269e2f768bf1f669800ac3c7a1d/dreamlet.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: Microarray 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... * Checking for pinned package versions... * Checking DESCRIPTION/NAMESPACE consistency... * Checking .Rbuildignore... * Checking for stray BiocCheck output folders... * Checking vignette directory... * NOTE: 'sessionInfo' not found in vignette(s) * Checking whether vignette is built with 'R CMD build'... * Checking package installation calls in R code... Warning in tools::parse_Rd(infile) : /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmptpHVA7/file14eb06492de24/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite' Warning in tools::parse_Rd(infile) : /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmptpHVA7/file14eb06492de24/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite' Warning in tools::parse_Rd(infile) : /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmptpHVA7/file14eb06492de24/dreamlet/man/run_mash.Rd:103: unknown macro '\insertAllCited' Warning in tools::parse_Rd(infile) : /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmptpHVA7/file14eb06492de24/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite' Warning in tools::parse_Rd(infile) : /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmptpHVA7/file14eb06492de24/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite' * Checking for library/require of dreamlet... * Checking coding practice... * NOTE: Avoid 1:...; use seq_len() or seq_along() * NOTE: Avoid using '=' for assignment and use '<-' instead * Checking parsed R code in R directory, examples, vignettes... * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times) * Checking function lengths... * NOTE: The recommended function length is 50 lines or less. There are 18 functions greater than 50 lines. * Checking man page documentation... Warning in tools::parse_Rd(manpage) : /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmptpHVA7/file14eb06492de24/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite' Warning in tools::parse_Rd(manpage) : /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmptpHVA7/file14eb06492de24/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite' Warning in tools::parse_Rd(manpage) : /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmptpHVA7/file14eb06492de24/dreamlet/man/run_mash.Rd:103: unknown macro '\insertAllCited' Warning in tools::parse_Rd(manpage) : /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmptpHVA7/file14eb06492de24/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite' Warning in tools::parse_Rd(manpage) : /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmptpHVA7/file14eb06492de24/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite' * WARNING: Empty or missing \value sections found in man pages. Warning in tools::parse_Rd(manpage) : /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmptpHVA7/file14eb06492de24/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite' Warning in tools::parse_Rd(manpage) : /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmptpHVA7/file14eb06492de24/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite' Warning in tools::parse_Rd(manpage) : /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmptpHVA7/file14eb06492de24/dreamlet/man/run_mash.Rd:103: unknown macro '\insertAllCited' Warning in tools::parse_Rd(manpage) : /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmptpHVA7/file14eb06492de24/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite' Warning in tools::parse_Rd(manpage) : /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmptpHVA7/file14eb06492de24/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite' Warning in tools::parse_Rd(manpage) : /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmptpHVA7/file14eb06492de24/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite' Warning in tools::parse_Rd(manpage) : /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmptpHVA7/file14eb06492de24/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite' Warning in tools::parse_Rd(manpage) : /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmptpHVA7/file14eb06492de24/dreamlet/man/run_mash.Rd:103: unknown macro '\insertAllCited' Warning in tools::parse_Rd(manpage) : /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmptpHVA7/file14eb06492de24/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite' Warning in tools::parse_Rd(manpage) : /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmptpHVA7/file14eb06492de24/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite' * 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; 407 lines (4%) are > 80 characters long. * NOTE: Consider 4 spaces instead of tabs; 1903 lines (19%) contain tabs. * NOTE: Consider multiples of 4 spaces for line indents; 518 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 ── 0 ERRORS | 1 WARNINGS | 9 NOTES See the dreamlet.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details.
lconway BUILD BIN output
=============================== R CMD BUILD =============================== >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir dreamlet_0.99.20.tar.gz' >>>>>>> * installing *source* package ‘dreamlet’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c colsum_beachmat.cpp -o colsum_beachmat.o In file included from colsum_beachmat.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/beachmat.h:24: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:218:43: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual] virtual sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5) virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5) virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:236:43: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual] virtual sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5) virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5) virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:254:46: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual] virtual sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5) virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5) virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:272:46: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual] virtual sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5) virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5) virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:287:35: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual] sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i) { ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3) virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3) virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:304:35: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual] sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i) { ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3) virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3) virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:321:38: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual] sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i) { ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3) virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3) virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:338:38: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual] sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i) { ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3) virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3) virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0; ^ 8 warnings generated. clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o dreamlet.so RcppExports.o colsum_beachmat.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/pkgbuild/packagebuilder/workers/jobs/2955/4d4000c52bd5c269e2f768bf1f669800ac3c7a1d/libdir/00LOCK-dreamlet/00new/dreamlet/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (dreamlet) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR libdir/dreamlet/libs/dreamlet.so >>>>>>> >>>>>>> Paths before fix: libdir/dreamlet/libs/dreamlet.so: dreamlet.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgcc_s.1.1.dylib" "libdir/dreamlet/libs/dreamlet.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgfortran.5.dylib" "libdir/dreamlet/libs/dreamlet.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libquadmath.0.dylib" "libdir/dreamlet/libs/dreamlet.so" >>>>>>> Paths after fix: libdir/dreamlet/libs/dreamlet.so: dreamlet.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)