CRAN Package Check Results for Maintainer ‘Henrik Bengtsson <henrikb at braju.com>’

Last updated on 2022-08-12 19:53:34 CEST.

Package FAIL WARN NOTE OK
ACNE 13
aroma.affymetrix 8 5
aroma.apd 1 12
aroma.cn 1 12
aroma.core 13
calmate 13
dChipIO 13
doFuture 13
future 2 11
future.apply 2 11
future.batchtools 1 12
future.callr 13
future.tests 13
globals 13
listenv 13
matrixStats 13
parallelly 13
profmem 13
progressr 2 11
PSCBS 13
R.cache 13
R.devices 1 12
R.filesets 13
R.huge 13
R.matlab 2 4 7
R.methodsS3 13
R.oo 13
R.rsp 1 12
R.utils 13
startup 13
TopDom 13

Package ACNE

Current CRAN status: OK: 13

Package aroma.affymetrix

Current CRAN status: NOTE: 8, OK: 5

Version: 3.2.1
Check: installed package size
Result: NOTE
     installed size is 5.8Mb
     sub-directories of 1Mb or more:
     R 2.3Mb
     help 1.1Mb
     testScripts 1.3Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 3.2.1
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'affxparser', 'oligo', 'oligoClasses', 'pdInfoBuilder',
     'AffymetrixDataTestFiles'
Flavor: r-release-macos-arm64

Version: 3.2.1
Check: Rd cross-references
Result: NOTE
    Packages unavailable to check Rd xrefs: ‘affxparser’, ‘oligo’, ‘oligoClasses’
Flavor: r-release-macos-arm64

Package aroma.apd

Current CRAN status: NOTE: 1, OK: 12

Version: 0.6.1
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘affxparser’
Flavor: r-release-macos-arm64

Version: 0.6.1
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘affxparser’
Flavor: r-release-macos-arm64

Package aroma.cn

Current CRAN status: NOTE: 1, OK: 12

Version: 1.7.0
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘GLAD’
Flavor: r-oldrel-macos-arm64

Package aroma.core

Current CRAN status: NOTE: 13

Version: 3.2.2
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-windows-ix86+x86_64

Version: 3.2.2
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'GLAD', 'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Version: 3.2.2
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘GLAD’
Flavor: r-oldrel-macos-arm64

Package calmate

Current CRAN status: OK: 13

Package dChipIO

Current CRAN status: OK: 13

Package doFuture

Current CRAN status: OK: 13

Package future

Current CRAN status: NOTE: 2, OK: 11

Version: 1.27.0
Check: HTML version of manual
Result: NOTE
    Found the following HTML validation problems:
    future.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
    future.html:23:4: Warning: <img> attribute "align" not allowed for HTML5
    multiprocess.html:28:1: Warning: nested emphasis <em>
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Package future.apply

Current CRAN status: NOTE: 2, OK: 11

Version: 1.9.0
Check: HTML version of manual
Result: NOTE
    Found the following HTML validation problems:
    future.apply.html:77:104: Warning: inserting implicit <p>
    future.apply.html:80:43: Warning: inserting implicit <p>
    future.apply.html:84:48: Warning: inserting implicit <p>
    future.apply.html:89:58: Warning: inserting implicit <p>
    future.apply.html:95:94: Warning: inserting implicit <p>
    future.apply.html:99:79: Warning: inserting implicit <p>
    future.apply.html:77:104: Warning: trimming empty <p>
    future.apply.html:80:43: Warning: trimming empty <p>
    future.apply.html:84:48: Warning: trimming empty <p>
    future.apply.html:89:58: Warning: trimming empty <p>
    future.apply.html:95:94: Warning: trimming empty <p>
    future.apply.html:99:79: Warning: trimming empty <p>
    future_lapply.html:303:105: Warning: inserting implicit <p>
    future_lapply.html:303:105: Warning: trimming empty <p>
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Package future.batchtools

Current CRAN status: NOTE: 1, OK: 12

Version: 0.10.0
Check: Rd cross-references
Result: NOTE
    Undeclared package ‘globals’ in Rd xrefs
Flavor: r-devel-linux-x86_64-fedora-clang

Package future.callr

Current CRAN status: OK: 13

Package future.tests

Current CRAN status: OK: 13

Package globals

Current CRAN status: OK: 13

Package listenv

Current CRAN status: OK: 13

Package matrixStats

Current CRAN status: OK: 13

Package parallelly

Current CRAN status: OK: 13

Package profmem

Current CRAN status: OK: 13

Package progressr

Current CRAN status: NOTE: 2, OK: 11

Version: 0.10.1
Check: HTML version of manual
Result: NOTE
    Found the following HTML validation problems:
    handlers.html:80:4: Warning: nested emphasis <em>
    with_progress.html:102:4: Warning: nested emphasis <em>
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Package PSCBS

Current CRAN status: OK: 13

Package R.cache

Current CRAN status: OK: 13

Package R.devices

Current CRAN status: WARN: 1, OK: 12

Version: 2.17.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building 'R.devices-overview.tex.rsp' using rsp
    R.devices v2.17.1 (2022-06-21 08:00:02 UTC) successfully loaded. See ?R.devices for help.
    Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "", :
     running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "R.devices-overview.tex" --max-iterations=20 -I "d:/RCompile/CRANpkg/local/4.1/R.devices.Rcheck/vign_test/R.devices/vignettes" -I "D:/RCompile/recent/R-4.1.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-4.1.3/share/texmf/bibtex/bst"' had status 1
    Error: processing vignette 'R.devices-overview.tex.rsp' failed with diagnostics:
    running 'texi2dvi' on 'R.devices-overview.tex' failed
    
    LaTeX errors:
    devices-overview.tex:55: LaTeX Error: Missing \begin{document}.
    
    See the LaTeX manual or LaTeX Companion for explanation.
    Type H <return> for immediate help
    You're in trouble here. Try typing <return> to proceed.
    
    --- failed re-building 'R.devices-overview.tex.rsp'
    
    SUMMARY: processing the following file failed:
     'R.devices-overview.tex.rsp'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Package R.filesets

Current CRAN status: OK: 13

Package R.huge

Current CRAN status: OK: 13

Package R.matlab

Current CRAN status: FAIL: 2, NOTE: 4, OK: 7

Version: 3.6.2
Check: HTML version of manual
Result: NOTE
    Found the following HTML validation problems:
    1._The_MATLAB_server_running_in_MATLAB.html:482:8: Warning: trimming empty <p>
    1._The_MATLAB_server_running_in_MATLAB.html:563:8: Warning: trimming empty <p>
    R.matlab-package.html:103:1: Warning: trimming empty <p>
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 3.6.2
Check: tests
Result: FAIL
    Check process probably crashed or hung up for 20 minutes ... killed
    Most likely this happened in the example checks (?),
    if not, ignore the following last lines of example output:
    Warning: R.methodsS3::throw() is deprecated. Use base::stop() instead, or R.oo::throw().
    ERROR: Detected objects with duplicated names (A). Only the last occurance of each duplicated object will be available in MATLAB if completed: writeMat.default(filename, A = A, B = B, A = C)
    >
    >
    > ## Not run:
    > ##D # When writing to a stream connection the receiver needs to know on
    > ##D # beforehand how many bytes are available. This can be done by using
    > ##D # the 'onWrite' argument.
    > ##D onWrite <- function(x)
    > ##D writeBin(x$length, con = x$con, size = 4, endian = "little")
    > ##D writeMat(con, A = A, B = B, onWrite = onWrite)
    > ## End(Not run)
    >
    >
    >
    > ### * <FOOTER>
    > ###
    > cleanEx()
    > options(digits = 7L)
    > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
    Time elapsed: 90.51 290.51 385.83 NA NA
    > grDevices::dev.off()
    null device
     1
    > ###
    > ### Local variables: ***
    > ### mode: outline-minor ***
    > ### outline-regexp: "\\(> \\)?### [*]+" ***
    > ### End: ***
    > quit('no')
    ======== End of example output (where/before crash/hang up occured ?) ========
Flavor: r-devel-windows-x86_64

Version: 3.6.2
Check: HTML version of manual
Result: NOTE
    Found the following problems:
    1._The_MATLAB_server_running_in_MATLAB.Rd:482:8: Warning: trimming empty <p>
    1._The_MATLAB_server_running_in_MATLAB.Rd:563:8: Warning: trimming empty <p>
    R.matlab-package.Rd:103:1: Warning: trimming empty <p>
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64

Version: 3.6.2
Check: tests
Result: FAIL
    Check process probably crashed or hung up for 20 minutes ... killed
    Most likely this happened in the example checks (?),
    if not, ignore the following last lines of example output:
    Warning: R.methodsS3::throw() is deprecated. Use base::stop() instead, or R.oo::throw().
    ERROR: Detected objects with duplicated names (A). Only the last occurance of each duplicated object will be available in MATLAB if completed: writeMat.default(filename, A = A, B = B, A = C)
    >
    >
    > ## Not run:
    > ##D # When writing to a stream connection the receiver needs to know on
    > ##D # beforehand how many bytes are available. This can be done by using
    > ##D # the 'onWrite' argument.
    > ##D onWrite <- function(x)
    > ##D writeBin(x$length, con = x$con, size = 4, endian = "little")
    > ##D writeMat(con, A = A, B = B, onWrite = onWrite)
    > ## End(Not run)
    >
    >
    >
    > ### * <FOOTER>
    > ###
    > cleanEx()
    > options(digits = 7L)
    > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
    Time elapsed: 116.81 340.08 460.37 NA NA
    > grDevices::dev.off()
    null device
     1
    > ###
    > ### Local variables: ***
    > ### mode: outline-minor ***
    > ### outline-regexp: "\\(> \\)?### [*]+" ***
    > ### End: ***
    > quit('no')
    ======== End of example output (where/before crash/hang up occured ?) ========
Flavor: r-release-windows-x86_64

Package R.methodsS3

Current CRAN status: OK: 13

Package R.oo

Current CRAN status: OK: 13

Package R.rsp

Current CRAN status: WARN: 1, OK: 12

Version: 0.45.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building 'R_packages-Static_PDF_and_HTML_vignettes.pdf.asis' using asis
    --- finished re-building 'R_packages-Static_PDF_and_HTML_vignettes.pdf.asis'
    
    --- re-building 'R_packages-LaTeX_vignettes.ltx' using tex
    Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "", :
     running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "R_packages-LaTeX_vignettes.ltx" --max-iterations=20 -I "D:/RCompile/recent/R-4.1.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-4.1.3/share/texmf/bibtex/bst"' had status 1
    Error: processing vignette 'R_packages-LaTeX_vignettes.ltx' failed with diagnostics:
    running 'texi2dvi' on 'R_packages-LaTeX_vignettes.ltx' failed
    
    LaTeX errors:
    -LaTeX_vignettes.ltx:21: LaTeX Error: Missing \begin{document}.
    
    See the LaTeX manual or LaTeX Companion for explanation.
    Type H <return> for immediate help
    You're in trouble here. Try typing <return> to proceed.
    
    --- failed re-building 'R_packages-LaTeX_vignettes.ltx'
    
    --- re-building 'Dynamic_document_creation_using_RSP.tex.rsp' using rsp
    Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "", :
     running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "Dynamic_document_creation_using_RSP.tex" --max-iterations=20 -I "d:/RCompile/CRANpkg/local/4.1/R.rsp.Rcheck/vign_test/R.rsp/vignettes" -I "D:/RCompile/recent/R-4.1.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-4.1.3/share/texmf/bibtex/bst"' had status 1
    Error: processing vignette 'Dynamic_document_creation_using_RSP.tex.rsp' failed with diagnostics:
    running 'texi2dvi' on 'Dynamic_document_creation_using_RSP.tex' failed
    
    LaTeX errors:
    cument_creation_using_RSP.tex:20: LaTeX Error: Missing \begin{document}.
    
    See the LaTeX manual or LaTeX Companion for explanation.
    Type H <return> for immediate help
    You're in trouble here. Try typing <return> to proceed.
    
    --- failed re-building 'Dynamic_document_creation_using_RSP.tex.rsp'
    
    --- re-building 'RSP_intro.html.rsp' using rsp
    --- finished re-building 'RSP_intro.html.rsp'
    
    --- re-building 'RSP_refcard.tex.rsp' using rsp
    Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "", :
     running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "RSP_refcard.tex" --max-iterations=20 -I "d:/RCompile/CRANpkg/local/4.1/R.rsp.Rcheck/vign_test/R.rsp/vignettes" -I "D:/RCompile/recent/R-4.1.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-4.1.3/share/texmf/bibtex/bst"' had status 1
    Error: processing vignette 'RSP_refcard.tex.rsp' failed with diagnostics:
    running 'texi2dvi' on 'RSP_refcard.tex' failed
    
    LaTeX errors:
    d.tex:19: LaTeX Error: Missing \begin{document}.
    
    See the LaTeX manual or LaTeX Companion for explanation.
    Type H <return> for immediate help
    You're in trouble here. Try typing <return> to proceed.
    
    --- failed re-building 'RSP_refcard.tex.rsp'
    
    --- re-building 'R_packages-RSP_vignettes.md.rsp' using rsp
    --- finished re-building 'R_packages-RSP_vignettes.md.rsp'
    
    --- re-building 'R_packages-Vignettes_prior_to_R300.tex.rsp' using rsp
    Warning in file(con, "r") :
     file("") only supports open = "w+" and open = "w+b": using the former
    Warning in file(con, "r") :
     file("") only supports open = "w+" and open = "w+b": using the former
    Warning in file(con, "r") :
     file("") only supports open = "w+" and open = "w+b": using the former
    Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "", :
     running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "R_packages-Vignettes_prior_to_R300.tex" --max-iterations=20 -I "d:/RCompile/CRANpkg/local/4.1/R.rsp.Rcheck/vign_test/R.rsp/vignettes" -I "D:/RCompile/recent/R-4.1.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-4.1.3/share/texmf/bibtex/bst"' had status 1
    Error: processing vignette 'R_packages-Vignettes_prior_to_R300.tex.rsp' failed with diagnostics:
    running 'texi2dvi' on 'R_packages-Vignettes_prior_to_R300.tex' failed
    
    LaTeX errors:
    -Vignettes_prior_to_R300.tex:16: LaTeX Error: Missing \begin{document}.
    
    See the LaTeX manual or LaTeX Companion for explanation.
    Type H <return> for immediate help
    You're in trouble here. Try typing <return> to proceed.
    
    --- failed re-building 'R_packages-Vignettes_prior_to_R300.tex.rsp'
    
    SUMMARY: processing the following files failed:
     'R_packages-LaTeX_vignettes.ltx'
     'Dynamic_document_creation_using_RSP.tex.rsp' 'RSP_refcard.tex.rsp'
     'R_packages-Vignettes_prior_to_R300.tex.rsp'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Package R.utils

Current CRAN status: OK: 13

Package startup

Current CRAN status: OK: 13

Package TopDom

Current CRAN status: OK: 13