Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/xcore
Last Changed Rev:  / Revision: 
Last Changed Date: 

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
merida1 macOS 10.14.6 Mojave/x86_64   OK     ERROR     OK     OK  
nebbiolo1 Linux (Ubuntu 20.04.4 LTS)/x86_64   OK     OK     skipped     OK  

merida1 Summary

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Package: xcore
Version: 0.99.3
RVersion: 4.2
BiocVersion: 3.15
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data xcore
BuildTime: 2 minutes 23.87 seconds
CheckCommand: BiocCheckGitClone('xcore') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch xcore_0.99.3.tar.gz && BiocCheck('xcore_0.99.3.tar.gz', `new-package`=TRUE)
CheckTime: 11 minutes 22.75 seconds
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh xcore_0.99.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir
BuildBinTime: 0 minutes 35.42 seconds
PackageFileSize: 1734.50 KiB
BuildID:: xcore_20220222072509
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: xcore. Starting Build package. Starting Check package. Starting Build package.
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 1. Build Package status: 0.

merida1 BUILD SRC output

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===============================

 R CMD BUILD

===============================

* checking for file ‘xcore/DESCRIPTION’ ... OK
* preparing ‘xcore’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘xcore_0.99.3.tar.gz’


merida1 CHECK output

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===============================

 BiocCheckGitClone('xcore')

===============================

This is BiocCheckGitClone version 1.31.34. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...


Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output




===============================

 R CMD CHECK

===============================

* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2496/01ac4642912724b98ba5e9c632dad8bd29fe3f55/xcore.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘xcore/DESCRIPTION’ ... OK
* this is package ‘xcore’ version ‘0.99.3’
* 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 ‘xcore’ can be installed ... [38s/40s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... 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 loading without being on the library search path ... 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 ... [37s/37s] NOTE
modelGeneExpression: no visible binding for global variable ‘offset’
modelGeneExpression_ridge_regression_wraper: no visible binding for
  global variable ‘y’
Undefined global functions or variables:
  offset y
Consider adding
  importFrom("stats", "offset")
to your NAMESPACE file.
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [242s/246s] OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
modelGeneExpression 215.025   1.62  219.72
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [141s/142s]
 [141s/142s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
  > library(testthat)
  > library(xcore)
  > 
  > test_check("xcore")
  model.frame(formula = mpg ~ ., data = mtcars)
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 61 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_processing.R:107:3): addSignatures ────────────────────────────
  digest::digest(mae) (`actual`) not equal to "b1493e0edf55d3347b328d6928ab15fb" (`expected`).
  
  `actual`:   "1d7c13819efc13aeab88f34d06dfc5a3"
  `expected`: "b1493e0edf55d3347b328d6928ab15fb"
  ── Failure (test_stats.R:269:3): modelGeneExpression ───────────────────────────
  digest::digest(res) (`actual`) not equal to "d650ad7e3f963bbf4d9e29b4457aa392" (`expected`).
  
  `actual`:   "98d93ead7e362572773d4a6ed7dae6cf"
  `expected`: "d650ad7e3f963bbf4d9e29b4457aa392"
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 61 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2496/01ac4642912724b98ba5e9c632dad8bd29fe3f55/xcore.Rcheck/00check.log’
for details.





===============================

 BiocCheck('xcore_0.99.3.tar.gz')

===============================

This is BiocCheck version 1.31.34. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
  running command 'R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' -q --vanilla --slave -f /Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocCheck/script/checkBadDeps.R --args "/Users/pkgbuild/packagebuilder/workers/jobs/2496/01ac4642912724b98ba5e9c632dad8bd29fe3f55/xcore_0.99.3.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpPYpVyl/file3d3375ad7bb8/lib" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* 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:
      Transcription, ChipOnChip
See http://bioconductor.org/developers/how-to/biocViews/
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
    * 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 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 vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of xcore...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 7
      times)
        suppressMessages() in R/processing.R (line 308, column 5)
        suppressWarnings() in R/stats.R (line 400, column 26)
        suppressWarnings() in R/stats.R (line 469, column 26)
        suppressWarnings() in R/stats.R (line 475, column 26)
        suppressMessages() in R/stats.R (line 400, column 43)
        suppressMessages() in R/stats.R (line 469, column 43)
        suppressMessages() in R/stats.R (line 475, column 43)
* Checking function lengths...
    * NOTE: Recommended function length <= 50 lines.
      There are 2 functions > 50 lines.
      The longest 5 functions are:
        modelGeneExpression() (R/stats.R, line 229): 130 lines
        modelGeneExpression_ridge_regression_wraper() (R/stats.R, line
      382): 53 lines
        modelGeneExpression_significance_testing_wraper() (R/stats.R,
      line 456): 48 lines
        prepareCountsForRegression() (R/processing.R, line 57): 39
      lines
        addSignatures() (R/processing.R, line 140): 32 lines
* Checking man page documentation...
    * NOTE: Consider adding runnable examples to the following man
      pages which document exported objects:
      pipe.Rd
    * NOTE: Usage of dontrun{} / donttest{} found in man page examples.
      4% of man pages use one of these cases.
      Found in the following files:
        design2factor.Rd
    * NOTE: Use donttest{} instead of dontrun{}.
      Found in the following files:
        design2factor.Rd
* Checking package NEWS...
    * NOTE: Consider adding a NEWS file, so your package news will be
      included in Bioconductor release announcements.
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 80 lines (3%) are > 80 characters
      long.
    First 6 lines:
      R/processing.R:4 #' \href{https://bioconductor.org/packages/release/bio...
      R/processing.R:6 #' normalized for the library size and transformed int...
      R/processing.R:25 #'     \item{U}{matrix giving expression values avera...
      R/processing.R:63   stopifnot("counts must be an integer matrix" = is.m...
      R/processing.R:64   stopifnot("design must be a matrix" = is.matrix(des...
      R/processing.R:65   stopifnot("number of rows in design must equal to n...
    * NOTE: Consider multiples of 4 spaces for line indents, 483
      lines(19%) are not.
    First 6 lines:
      R/processing.R:58                                        design,
      R/processing.R:59                                        base_lvl,
      R/processing.R:60                                        log2 = TRUE,
      R/processing.R:61                                        pseudo_count =...
      R/processing.R:62                                        drop_base_lvl ...
      R/processing.R:63   stopifnot("counts must be an integer matrix" = is.m...
    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 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.


Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 10
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output

merida1 BUILD BIN output

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===============================

 R CMD BUILD

===============================

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir xcore_0.99.3.tar.gz'
>>>>>>> 

* installing *source* package ‘xcore’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to '>=' 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (xcore)



nebbiolo1 Summary

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Package: xcore
Version: 0.99.3
RVersion: 4.2
BiocVersion: 3.15
BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data xcore
BuildTime: 0 minutes 57.97 seconds
CheckCommand: BiocCheckGitClone('xcore') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings xcore_0.99.3.tar.gz && BiocCheck('xcore_0.99.3.tar.gz', `new-package`=TRUE)
CheckTime: 5 minutes 41.42 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 1737.54 KiB
BuildID:: xcore_20220222072509
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: xcore. 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.

nebbiolo1 BUILD SRC output

[top]

===============================

 R CMD BUILD

===============================

* checking for file ‘xcore/DESCRIPTION’ ... OK
* preparing ‘xcore’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘xcore_0.99.3.tar.gz’


nebbiolo1 CHECK output

[top]

===============================

 BiocCheckGitClone('xcore')

===============================

This is BiocCheckGitClone version 1.31.34. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...


Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output




===============================

 R CMD CHECK

===============================

* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2496/01ac4642912724b98ba5e9c632dad8bd29fe3f55/xcore.Rcheck’
* using R Under development (unstable) (2022-02-17 r81757)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘xcore/DESCRIPTION’ ... OK
* this is package ‘xcore’ version ‘0.99.3’
* 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 ‘xcore’ can be installed ... [13s/13s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... 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 loading without being on the library search path ... 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 ... [15s/15s] NOTE
modelGeneExpression: no visible binding for global variable ‘offset’
modelGeneExpression_ridge_regression_wraper: no visible binding for
  global variable ‘y’
Undefined global functions or variables:
  offset y
Consider adding
  importFrom("stats", "offset")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [150s/150s] OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
modelGeneExpression 138.04  0.807 138.856
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [81s/81s]
 [81s/81s] 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: 1 NOTE
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/2496/01ac4642912724b98ba5e9c632dad8bd29fe3f55/xcore.Rcheck/00check.log’
for details.






===============================

 BiocCheck('xcore_0.99.3.tar.gz')

===============================

This is BiocCheck version 1.31.34. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
  running command 'R_DEFAULT_PACKAGES=NULL '/home/biocbuild/bbs-3.15-bioc/R/bin/R' -q --vanilla --slave -f /home/biocbuild/bbs-3.15-bioc/R/library/BiocCheck/script/checkBadDeps.R --args "/home/pkgbuild/packagebuilder/workers/jobs/2496/01ac4642912724b98ba5e9c632dad8bd29fe3f55/xcore_0.99.3.tar.gz" "/tmp/Rtmpby3Hxf/file3884da518a400f/lib" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* 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:
      Transcription, ChipOnChip
See http://bioconductor.org/developers/how-to/biocViews/
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
    * 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 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 vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of xcore...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 7
      times)
        suppressMessages() in R/processing.R (line 308, column 5)
        suppressWarnings() in R/stats.R (line 400, column 26)
        suppressWarnings() in R/stats.R (line 469, column 26)
        suppressWarnings() in R/stats.R (line 475, column 26)
        suppressMessages() in R/stats.R (line 400, column 43)
        suppressMessages() in R/stats.R (line 469, column 43)
        suppressMessages() in R/stats.R (line 475, column 43)
* Checking function lengths...
    * NOTE: Recommended function length <= 50 lines.
      There are 2 functions > 50 lines.
      The longest 5 functions are:
        modelGeneExpression() (R/stats.R, line 229): 130 lines
        modelGeneExpression_ridge_regression_wraper() (R/stats.R, line
      382): 53 lines
        modelGeneExpression_significance_testing_wraper() (R/stats.R,
      line 456): 48 lines
        prepareCountsForRegression() (R/processing.R, line 57): 39
      lines
        addSignatures() (R/processing.R, line 140): 32 lines
* Checking man page documentation...
    * NOTE: Consider adding runnable examples to the following man
      pages which document exported objects:
      pipe.Rd
    * NOTE: Usage of dontrun{} / donttest{} found in man page examples.
      4% of man pages use one of these cases.
      Found in the following files:
        design2factor.Rd
    * NOTE: Use donttest{} instead of dontrun{}.
      Found in the following files:
        design2factor.Rd
* Checking package NEWS...
    * NOTE: Consider adding a NEWS file, so your package news will be
      included in Bioconductor release announcements.
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 80 lines (3%) are > 80 characters
      long.
    First 6 lines:
      R/processing.R:4 #' \href{https://bioconductor.org/packages/release/bio...
      R/processing.R:6 #' normalized for the library size and transformed int...
      R/processing.R:25 #'     \item{U}{matrix giving expression values avera...
      R/processing.R:63   stopifnot("counts must be an integer matrix" = is.m...
      R/processing.R:64   stopifnot("design must be a matrix" = is.matrix(des...
      R/processing.R:65   stopifnot("number of rows in design must equal to n...
    * NOTE: Consider multiples of 4 spaces for line indents, 483
      lines(19%) are not.
    First 6 lines:
      R/processing.R:58                                        design,
      R/processing.R:59                                        base_lvl,
      R/processing.R:60                                        log2 = TRUE,
      R/processing.R:61                                        pseudo_count =...
      R/processing.R:62                                        drop_base_lvl ...
      R/processing.R:63   stopifnot("counts must be an integer matrix" = is.m...
    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 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.


Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 10
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output

nebbiolo1 BUILD BIN output

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