Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* 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_0.99.6.tar.gz'

Installing package prior to check...


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 BiocCheckGitClone('APAlog')

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This is BiocCheckGitClone version 1.27.2. 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/3.13/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output




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 R CMD CHECK

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* using log directory 'C:/Users/pkgbuild/packagebuilder/workers/jobs/1952/2984611c755855665cafa3ed37c939fa3d08168c/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 '0.99.6'
* 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 whether package 'APAlog' can be installed ... 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
* 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 ... [9s] 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 ... NOTE
Rd file 'adj_p.Rd':
  \examples lines wider than 100 characters:
     fit1_pA <- pA_multi_logit(pA.toy2, pA.site ~ cell_line, pA_design, "sample", long_output = FALSE, adj_method='fdr')

Rd file 'pA_multi_logit.Rd':
  \examples lines wider than 100 characters:
     fit1_pA <- pA_multi_logit(pA.toy2, pA.site ~ cell_line, pA_design, "sample", long_output = FALSE, adj_method='fdr')

Rd file 'volcano_plot.Rd':
  \examples lines wider than 100 characters:
     fit1 <- pA_multi_logit(APAlog::pA.toy2, pA.site ~ cell_line, APAlog::pA_design, "sample", adj_method='fdr')

These lines will be truncated in the PDF manual.
* 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 ...
** running examples for arch 'i386' ... [3s] ERROR
Running examples in 'APAlog-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: volcano_plot
> ### Title: volcano_plot
> ### Aliases: volcano_plot
> 
> ### ** Examples
> 
> fit1 <- pA_multi_logit(APAlog::pA.toy2, pA.site ~ cell_line, APAlog::pA_design, "sample", adj_method='fdr')
[1] "0% of transcripts had <2 active pA sites and were removed"
# weights:  3 (2 variable)
initial  value 29.927729 
final  value 26.512164 
converged
# weights:  3 (2 variable)
initial  value 51.128270 
final  value 47.404405 
converged
# weights:  12 (6 variable)
initial  value 284.430435 
iter  10 value 221.213446
final  value 221.207404 
converged
# weights:  3 (2 variable)
initial  value 21.026071 
final  value 20.830417 
converged
# weights:  3 (2 variable)
initial  value 123.327065 
iter  10 value 44.701920
final  value 44.701919 
converged
# weights:  3 (2 variable)
initial  value 84.199013 
final  value 83.243669 
converged
# weights:  3 (2 variable)
initial  value 18.125161 
final  value 12.648638 
converged
# weights:  3 (2 variable)
initial  value 114.856686 
final  value 32.731136 
converged
> 
> vplot <- volcano_plot(fit1, x='logfdr', y='p_values', xlab = "Ln fold change", ylab = "-Log10 FDR",
+ title = "LMCN data, metastatic vs non-metastatic", titleLabSize = 12, border = "full",
+ pCutoff = 0.001, FCcutoff = 1.5, xlim = c(-5, 5), ylim = c(0, 10))
[1] "The column logfdr does not exist in the given dataframe."
Error in volcano_plot(fit1, x = "logfdr", y = "p_values", xlab = "Ln fold change",  : 
  The column logfdr does not exist in the given dataframe.
Execution halted
** running examples for arch 'x64' ... [3s] ERROR
Running examples in 'APAlog-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: volcano_plot
> ### Title: volcano_plot
> ### Aliases: volcano_plot
> 
> ### ** Examples
> 
> fit1 <- pA_multi_logit(APAlog::pA.toy2, pA.site ~ cell_line, APAlog::pA_design, "sample", adj_method='fdr')
[1] "0% of transcripts had <2 active pA sites and were removed"
# weights:  3 (2 variable)
initial  value 29.927729 
final  value 26.512164 
converged
# weights:  3 (2 variable)
initial  value 51.128270 
final  value 47.404405 
converged
# weights:  12 (6 variable)
initial  value 284.430435 
iter  10 value 221.213446
final  value 221.207404 
converged
# weights:  3 (2 variable)
initial  value 21.026071 
final  value 20.830417 
converged
# weights:  3 (2 variable)
initial  value 123.327065 
iter  10 value 44.701920
final  value 44.701919 
converged
# weights:  3 (2 variable)
initial  value 84.199013 
final  value 83.243669 
converged
# weights:  3 (2 variable)
initial  value 18.125161 
final  value 12.648638 
converged
# weights:  3 (2 variable)
initial  value 114.856686 
final  value 32.731136 
converged
> 
> vplot <- volcano_plot(fit1, x='logfdr', y='p_values', xlab = "Ln fold change", ylab = "-Log10 FDR",
+ title = "LMCN data, metastatic vs non-metastatic", titleLabSize = 12, border = "full",
+ pCutoff = 0.001, FCcutoff = 1.5, xlim = c(-5, 5), ylim = c(0, 10))
[1] "The column logfdr does not exist in the given dataframe."
Error in volcano_plot(fit1, x = "logfdr", y = "p_values", xlab = "Ln fold change",  : 
  The column logfdr does not exist in the given dataframe.
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, 4 NOTEs
See
  'C:/Users/pkgbuild/packagebuilder/workers/jobs/1952/2984611c755855665cafa3ed37c939fa3d08168c/APAlog.Rcheck/00check.log'
for details.





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 BiocCheck('APAlog_0.99.6.tar.gz')

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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; 155 lines (21%) 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, 41
      lines(6%) are not.
    First 6 lines:
      man/pA_multi_logit.Rd:8   data,
      man/pA_multi_logit.Rd:9   model,
      man/pA_multi_logit.Rd:10   design = NULL,
      man/pA_multi_logit.Rd:11   sample_ID = NULL,
      man/pA_multi_logit.Rd:12   long_output = FALSE,
      man/pA_multi_logit.Rd:13   adj_method
    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

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 R CMD BUILD

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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 ]
    pA.toy2                                 html  
REDIRECT:topic	 pA.toy2 -> pA.toy2.html [ SUCCESS ]
    pA_design                               html  
REDIRECT:topic	 pA_design -> pA_design.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 ]
    volcano_plot                            html  
REDIRECT:topic	 volcano_plot -> volcano_plot.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_0.99.6.zip
* DONE (APAlog)