machv2 Summary
[top]
Package: APAlog |
Version: 0.99.1 |
RVersion: 4.1
|
BiocVersion: 3.13
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data APAlog |
BuildTime: 0 minutes 9.49 seconds |
CheckCommand: BiocCheckGitClone('APAlog') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch APAlog_0.99.1.tar.gz && BiocCheck('APAlog_0.99.1.tar.gz', `new-package`=TRUE) |
CheckTime: 0 minutes 50.65 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh APAlog_0.99.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 5.51 seconds |
PackageFileSize: 676.49 KiB |
BuildID:: APAlog_20210315001817 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: APAlog. Starting Build package. Starting Check package. Starting Build package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Checking Package status: 1. Build Package status: 0. |
machv2 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘APAlog/DESCRIPTION’ ... OK
* preparing ‘APAlog’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘APAlog_0.99.1.tar.gz’
machv2 CHECK output
[top]
===============================
BiocCheckGitClone('APAlog')
===============================
This is BiocCheckGitClone version 1.27.2. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* ERROR: System Files found that should not be git tracked:
APAlog.Rproj
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.13/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheckGitClone FAILED.
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/1952/e5643149b9ac4067fd42bbec40fa9a4bc2fe4dfa/APAlog.Rcheck’
* using R Under development (unstable) (2021-02-19 r80028)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘APAlog/DESCRIPTION’ ... OK
* this is package ‘APAlog’ version ‘0.99.1’
* 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 ... WARNING
Found the following file with a non-portable file name:
APALog _logo3.png
These are not fully portable file names.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘APAlog’ can be installed ... [5s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
MIT
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... [6s/6s] NOTE
remove_0_1_pA_transcripts: no visible binding for global variable
‘transcript’
Undefined global functions or variables:
transcript
* 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 ... WARNING
Undocumented code objects:
‘pA.toy2’ ‘pA_design’ ‘volcano_plot’
Undocumented data sets:
‘pA.toy2’ ‘pA_design’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'pA_logit_dev':
pA_logit_dev
Code: function(data, model, design = NULL, sample_ID = NULL,
adj_method)
Docs: function(data, model, design = NULL, sample_ID = NULL)
Argument names in code not in docs:
adj_method
Codoc mismatches from documentation object 'pA_multi_logit':
pA_multi_logit
Code: function(data, model, design = NULL, sample_ID = NULL,
long_output = FALSE, adj_method)
Docs: function(data, model, design = NULL, sample_ID = NULL,
long_output = FALSE)
Argument names in code not in docs:
adj_method
* 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 ... [1s/1s] ERROR
Running examples in ‘APAlog-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: adj_p
> ### Title: adj_p
> ### Aliases: adj_p
>
> ### ** Examples
>
> fit3_pA_fdr <- adj_p(fit3_pA, pcols = 2, adj_method = "fdr")
Error in adj_p(fit3_pA, pcols = 2, adj_method = "fdr") :
object 'fit3_pA' not found
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, 3 WARNINGs, 3 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/1952/e5643149b9ac4067fd42bbec40fa9a4bc2fe4dfa/APAlog.Rcheck/00check.log’
for details.
===============================
BiocCheck('APAlog_0.99.1.tar.gz')
===============================
This is BiocCheck version 1.27.2. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 1 object(s) are initialized. Maybe
it is part of a data set loaded with data(), or perhaps part of
an object referenced in with() or within().
function (object)
remove_0_1_pA_transcripts (transcript)
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* WARNING: Update R version dependency from 4.0 to 4.1.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking vignette directory...
This is a software package
* Checking whether vignette is built with 'R CMD build'...
* Checking library calls...
* Checking for library/require of APAlog...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths......
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 144 lines (23%) are > 80 characters
long.
First 6 lines:
R/Tests.R:11 #' @description Function to compare the usage of alternati...
R/Tests.R:12 #' @param data Dataset containing poly A (pA) site read co...
R/Tests.R:13 #' column containing read counts (and it MUST be named "co...
R/Tests.R:14 #' Thus, each row in \code{data} contains the read count f...
R/Tests.R:15 #' Other sample attributes beyond sample ID may be recorde...
R/Tests.R:16 #' and a key variable (e.g. sample ID) connecting the \cod...
* NOTE: Consider multiples of 4 spaces for line indents, 24
lines(4%) are not.
First 6 lines:
man/pA_multi_logit.Rd:8 long_output = FALSE)
vignettes/APAlog_tutorial.Rmd:6 %\VignetteIndexEntry{APAlog Tutorial}
vignettes/APAlog_tutorial.Rmd:7 %\VignetteEngine{knitr::rmarkdown}
vignettes/APAlog_tutorial.Rmd:8 \usepackage[utf8]{inputenc}
vignettes/APAlog_tutorial.Rmd:36 ...
vignettes/APAlog_tutorial.Rmd:37 ...
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.
Summary:
ERROR count: 0
WARNING count: 1
NOTE count: 4
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.13/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
machv2 BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir APAlog_0.99.1.tar.gz'
>>>>>>>
* installing *source* package ‘APAlog’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (APAlog)
tokay2 Summary
[top]
Package: APAlog |
Version: 0.99.1 |
RVersion: 4.1
|
BiocVersion: 3.13
|
BuildCommand: C:\Users\biocbuild\bbs-3.13-bioc\R\bin/R CMD build --keep-empty-dirs --no-resave-data APAlog |
BuildTime: 0 minutes 33.78 seconds |
CheckCommand: C:\Users\biocbuild\bbs-3.13-bioc\R\bin/R CMD INSTALL --build --merge-multiarch --library=APAlog.buildbin-libdir APAlog_0.99.1.tar.gz >APAlog-install.out 2>&1 && C:\Users\biocbuild\bbs-3.13-bioc\R\bin/R CMD check --library=APAlog.buildbin-libdir --install="check:APAlog-install.out" --force-multiarch --no-vignettes --timings APAlog_0.99.1.tar.gz && BiocCheck('APAlog_0.99.1.tar.gz', `new-package`=TRUE) |
CheckTime: 1 minutes 14.54 seconds |
BuildBinCommand: C:\Users\biocbuild\bbs-3.13-bioc\R\bin/R CMD INSTALL --build --merge-multiarch --library=APAlog.buildbin-libdir APAlog_0.99.1.tar.gz |
BuildBinTime: 0 minutes 10.31 seconds |
PackageFileSize: 680.99 KiB |
BuildID:: APAlog_20210315001817 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: APAlog. Starting Build package. Starting Check package. Starting Build package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Checking Package status: 0. Build Package status: 0. |
tokay2 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file 'APAlog/DESCRIPTION' ... OK
* preparing 'APAlog':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building 'APAlog_0.99.1.tar.gz'
tokay2 CHECK output
[top]
Installing package prior to check...
===============================
BiocCheckGitClone('APAlog')
===============================
This is BiocCheckGitClone version 1.27.2. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* ERROR: System Files found that should not be git tracked:
APAlog.Rproj
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.13/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheckGitClone FAILED.
===============================
R CMD CHECK
===============================
* using log directory 'C:/Users/pkgbuild/packagebuilder/workers/jobs/1952/e5643149b9ac4067fd42bbec40fa9a4bc2fe4dfa/APAlog.Rcheck'
* using R Under development (unstable) (2021-02-08 r79971)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'APAlog/DESCRIPTION' ... OK
* this is package 'APAlog' version '0.99.1'
* 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 ... WARNING
Found the following file with a non-portable file name:
APALog _logo3.png
These are not fully portable file names.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking whether package 'APAlog' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
MIT
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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
** checking loading without being on the library search path ... OK
** checking use of S3 registration ... 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 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 ... [8s] NOTE
remove_0_1_pA_transcripts: no visible binding for global variable
'transcript'
Undefined global functions or variables:
transcript
* checking Rd files ... [1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'pA.toy2' 'pA_design' 'volcano_plot'
Undocumented data sets:
'pA.toy2' 'pA_design'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'pA_logit_dev':
pA_logit_dev
Code: function(data, model, design = NULL, sample_ID = NULL,
adj_method)
Docs: function(data, model, design = NULL, sample_ID = NULL)
Argument names in code not in docs:
adj_method
Codoc mismatches from documentation object 'pA_multi_logit':
pA_multi_logit
Code: function(data, model, design = NULL, sample_ID = NULL,
long_output = FALSE, adj_method)
Docs: function(data, model, design = NULL, sample_ID = NULL,
long_output = FALSE)
Argument names in code not in docs:
adj_method
* 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 ...
** running examples for arch 'i386' ... [2s] ERROR
Running examples in 'APAlog-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: adj_p
> ### Title: adj_p
> ### Aliases: adj_p
>
> ### ** Examples
>
> fit3_pA_fdr <- adj_p(fit3_pA, pcols = 2, adj_method = "fdr")
Error in adj_p(fit3_pA, pcols = 2, adj_method = "fdr") :
object 'fit3_pA' not found
Execution halted
** running examples for arch 'x64' ... [2s] ERROR
Running examples in 'APAlog-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: adj_p
> ### Title: adj_p
> ### Aliases: adj_p
>
> ### ** Examples
>
> fit3_pA_fdr <- adj_p(fit3_pA, pcols = 2, adj_method = "fdr")
Error in adj_p(fit3_pA, pcols = 2, adj_method = "fdr") :
object 'fit3_pA' not found
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: 2 ERRORs, 3 WARNINGs, 4 NOTEs
See
'C:/Users/pkgbuild/packagebuilder/workers/jobs/1952/e5643149b9ac4067fd42bbec40fa9a4bc2fe4dfa/APAlog.Rcheck/00check.log'
for details.
===============================
BiocCheck('APAlog_0.99.1.tar.gz')
===============================
This is BiocCheck version 1.27.2. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 1 object(s) are initialized. Maybe
it is part of a data set loaded with data(), or perhaps part of
an object referenced in with() or within().
function (object)
remove_0_1_pA_transcripts (transcript)
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* WARNING: Update R version dependency from 4.0 to 4.1.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking vignette directory...
This is a software package
* Checking whether vignette is built with 'R CMD build'...
* Checking library calls...
* Checking for library/require of APAlog...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths......
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 144 lines (23%) are > 80 characters
long.
First 6 lines:
R/Tests.R:11 #' @description Function to compare the usage of alternati...
R/Tests.R:12 #' @param data Dataset containing poly A (pA) site read co...
R/Tests.R:13 #' column containing read counts (and it MUST be named "co...
R/Tests.R:14 #' Thus, each row in \code{data} contains the read count f...
R/Tests.R:15 #' Other sample attributes beyond sample ID may be recorde...
R/Tests.R:16 #' and a key variable (e.g. sample ID) connecting the \cod...
* NOTE: Consider multiples of 4 spaces for line indents, 24
lines(4%) are not.
First 6 lines:
man/pA_multi_logit.Rd:8 long_output = FALSE)
vignettes/APAlog_tutorial.Rmd:6 %\VignetteIndexEntry{APAlog Tutorial}
vignettes/APAlog_tutorial.Rmd:7 %\VignetteEngine{knitr::rmarkdown}
vignettes/APAlog_tutorial.Rmd:8 \usepackage[utf8]{inputenc}
vignettes/APAlog_tutorial.Rmd:36 ...
vignettes/APAlog_tutorial.Rmd:37 ...
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.
Summary:
ERROR count: 0
WARNING count: 1
NOTE count: 4
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.13/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
tokay2 BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
install for i386
* installing *source* package 'APAlog' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'APAlog'
finding HTML links ... done
adj_p html
REDIRECT:topic adj_p -> adj_p.html [ SUCCESS ]
glm_deviance_test_p html
REDIRECT:topic glm_deviance_test_p -> glm_deviance_test_p.html [ SUCCESS ]
pA_logit_1tr_pairs html
REDIRECT:topic pA_logit_1tr_pairs -> pA_logit_1tr_pairs.html [ SUCCESS ]
pA_logit_dev html
REDIRECT:topic pA_logit_dev -> pA_logit_dev.html [ SUCCESS ]
pA_logit_pairwise html
REDIRECT:topic pA_logit_pairwise -> pA_logit_pairwise.html [ SUCCESS ]
pA_multi_logit html
REDIRECT:topic pA_multi_logit -> pA_multi_logit.html [ SUCCESS ]
remove_0_1_pA_transcripts html
REDIRECT:topic remove_0_1_pA_transcripts -> remove_0_1_pA_transcripts.html [ SUCCESS ]
** 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 'APAlog' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'APAlog' as APAlog_0.99.1.zip
* DONE (APAlog)
malbec2 Summary
[top]
Package: APAlog |
Version: 0.99.1 |
RVersion: 4.1
|
BiocVersion: 3.13
|
BuildCommand: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data APAlog |
BuildTime: 0 minutes 11.22 seconds |
CheckCommand: BiocCheckGitClone('APAlog') && /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --no-vignettes --timings APAlog_0.99.1.tar.gz && BiocCheck('APAlog_0.99.1.tar.gz', `new-package`=TRUE) |
CheckTime: 0 minutes 37.27 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 705.12 KiB |
BuildID:: APAlog_20210315001817 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: APAlog. Starting Build package. Starting Check package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Checking Package status: 1. |
malbec2 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘APAlog/DESCRIPTION’ ... OK
* preparing ‘APAlog’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘APAlog_0.99.1.tar.gz’
malbec2 CHECK output
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===============================
BiocCheckGitClone('APAlog')
===============================
This is BiocCheckGitClone version 1.27.2. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* ERROR: System Files found that should not be git tracked:
APAlog.Rproj
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.13/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheckGitClone FAILED.
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/1952/e5643149b9ac4067fd42bbec40fa9a4bc2fe4dfa/APAlog.Rcheck’
* using R Under development (unstable) (2021-02-10 r79979)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘APAlog/DESCRIPTION’ ... OK
* this is package ‘APAlog’ version ‘0.99.1’
* 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 ... WARNING
Found the following file with a non-portable file name:
APALog _logo3.png
These are not fully portable file names.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘APAlog’ can be installed ... [4s/4s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
MIT
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... [5s/5s] NOTE
remove_0_1_pA_transcripts: no visible binding for global variable
‘transcript’
Undefined global functions or variables:
transcript
* 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 ... WARNING
Undocumented code objects:
‘pA.toy2’ ‘pA_design’ ‘volcano_plot’
Undocumented data sets:
‘pA.toy2’ ‘pA_design’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'pA_logit_dev':
pA_logit_dev
Code: function(data, model, design = NULL, sample_ID = NULL,
adj_method)
Docs: function(data, model, design = NULL, sample_ID = NULL)
Argument names in code not in docs:
adj_method
Codoc mismatches from documentation object 'pA_multi_logit':
pA_multi_logit
Code: function(data, model, design = NULL, sample_ID = NULL,
long_output = FALSE, adj_method)
Docs: function(data, model, design = NULL, sample_ID = NULL,
long_output = FALSE)
Argument names in code not in docs:
adj_method
* 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 ... [1s/1s] ERROR
Running examples in ‘APAlog-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: adj_p
> ### Title: adj_p
> ### Aliases: adj_p
>
> ### ** Examples
>
> fit3_pA_fdr <- adj_p(fit3_pA, pcols = 2, adj_method = "fdr")
Error in adj_p(fit3_pA, pcols = 2, adj_method = "fdr") :
object 'fit3_pA' not found
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, 3 WARNINGs, 4 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/1952/e5643149b9ac4067fd42bbec40fa9a4bc2fe4dfa/APAlog.Rcheck/00check.log’
for details.
===============================
BiocCheck('APAlog_0.99.1.tar.gz')
===============================
This is BiocCheck version 1.27.2. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 1 object(s) are initialized. Maybe
it is part of a data set loaded with data(), or perhaps part of
an object referenced in with() or within().
function (object)
remove_0_1_pA_transcripts (transcript)
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* WARNING: Update R version dependency from 4.0 to 4.1.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking vignette directory...
This is a software package
* Checking whether vignette is built with 'R CMD build'...
* Checking library calls...
* Checking for library/require of APAlog...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths......
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 144 lines (23%) are > 80 characters
long.
First 6 lines:
R/Tests.R:11 #' @description Function to compare the usage of alternati...
R/Tests.R:12 #' @param data Dataset containing poly A (pA) site read co...
R/Tests.R:13 #' column containing read counts (and it MUST be named "co...
R/Tests.R:14 #' Thus, each row in \code{data} contains the read count f...
R/Tests.R:15 #' Other sample attributes beyond sample ID may be recorde...
R/Tests.R:16 #' and a key variable (e.g. sample ID) connecting the \cod...
* NOTE: Consider multiples of 4 spaces for line indents, 24
lines(4%) are not.
First 6 lines:
man/pA_multi_logit.Rd:8 long_output = FALSE)
vignettes/APAlog_tutorial.Rmd:6 %\VignetteIndexEntry{APAlog Tutorial}
vignettes/APAlog_tutorial.Rmd:7 %\VignetteEngine{knitr::rmarkdown}
vignettes/APAlog_tutorial.Rmd:8 \usepackage[utf8]{inputenc}
vignettes/APAlog_tutorial.Rmd:36 ...
vignettes/APAlog_tutorial.Rmd:37 ...
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.
Summary:
ERROR count: 0
WARNING count: 1
NOTE count: 4
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.13/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
malbec2 BUILD BIN output
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