Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘LinTInd/DESCRIPTION’ ... OK
* preparing ‘LinTInd’:
* 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 ‘LinTInd_0.99.1.tar.gz’

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 BiocCheckGitClone('LinTInd')

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This is BiocCheckGitClone version 1.31.23. 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:
        LinTInd.Rproj
        .DS_Store
        data/.DS_Store
        inst/.DS_Store
        inst/extdata/.DS_Store
        man/.DS_Store
        vignettes/.DS_Store
* 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/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheckGitClone FAILED.




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 R CMD CHECK

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* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2468/5b6bced7f2c5c43821ab9b34dfa6c7c3d1ebdb73/LinTInd.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 ‘LinTInd/DESCRIPTION’ ... OK
* this is package ‘LinTInd’ 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 ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘LinTInd’ can be installed ... [15s/15s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:
  `use_mit_license()`, `use_gpl3_license()` or friends to pick a
  license
Standardizable: FALSE
* 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
TagDist: warning in pheatmap(t(clone_tab), cluster_cols = FALSE,
  cluster_rows = FALSE, show_colnames = FALSE, border = FALSE,
  annotation_col = annotation_col, scale = "row", filename =
  "tag_heatmap_scale.pdf", width = 5, height = 3): partial argument
  match of 'border' to 'border_color'
TagDist: warning in pheatmap(all_jac, file = "group_dist.pdf", width =
  4.9, height = 4.5): partial argument match of 'file' to 'filename'
TagDist: warning in pheatmap(-log2(all_p + min(all_p[all_p != 0])),
  main = "log2(P.val)", file = "group_dist.pdf", width = 4.9, height =
  4.7): partial argument match of 'file' to 'filename'
TagDist: warning in pheatmap(cor_s, file = "group_dist.pdf", width =
  4.9, height = 4.5): partial argument match of 'file' to 'filename'
BuildTree: no visible global function definition for ‘write.csv’
FindIndel : find_barcode: no visible global function definition for
  ‘is’
FindIndel: no visible global function definition for ‘write.table’
IndelForm: no visible global function definition for ‘write.csv’
IndelIdents: no visible global function definition for ‘write.csv’
IndelIdents : max_reads_stat: no visible global function definition for
  ‘is’
IndelPlot: no visible binding for global variable ‘Site’
IndelPlot: no visible binding for global variable ‘Freq’
PlotTree: no visible binding for global variable ‘tags’
PlotTree: no visible binding for global variable ‘celltype’
PlotTree: no visible binding for global variable ‘Freq’
PlotTree : SortTree: no visible binding for global variable
  ‘tag_number’
PlotTree: no visible binding for global variable ‘y’
PlotTree: no visible binding for global variable ‘variable’
PlotTree: no visible binding for global variable ‘value’
ReadFasta: no visible global function definition for ‘read.table’
TagProcess: no visible binding for global variable ‘i’
change_form_stat : <anonymous>: no visible binding for global variable
  ‘scarref’
change_form_stat: no visible binding for global variable ‘scarref’
Undefined global functions or variables:
  Freq Site celltype i is read.table scarref tag_number tags value
  variable write.csv write.table y
Consider adding
  importFrom("methods", "is")
  importFrom("utils", "read.table", "write.csv", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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:
  ‘cellsinfo’ ‘celltype’ ‘cutsite’ ‘data’ ‘ref’ ‘scarform’ ‘scarinfo’
  ‘scarref’ ‘scarref_all’ ‘tag’ ‘treeinfo’
Undocumented data sets:
  ‘cellsinfo’ ‘celltype’ ‘cutsite’ ‘data’ ‘ref’ ‘scarform’ ‘scarinfo’
  ‘scarref’ ‘scarref_all’ ‘tag’ ‘treeinfo’
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 'ReadCutsite':
ReadCutsite
  Code: function(segref, reftype = NULL)
  Docs: function(cutsite, reftype = "Accurate")
  Argument names in code not in docs:
    segref
  Argument names in docs not in code:
    cutsite
  Mismatches in argument names:
    Position: 1 Code: segref Docs: cutsite
  Mismatches in argument default values:
    Name: 'reftype' Code: NULL Docs: "Accurate"

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'ReadCutsite'
  ‘cutsite’
Documented arguments not in \usage in documentation object 'ReadCutsite':
  ‘segref’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                   old_size new_size compress
  example_data.rda    185Kb     79Kb       xz
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/4s] ERROR
Running examples in ‘LinTInd-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: FindIndel
> ### Title: FindIndel
> ### Aliases: FindIndel
> 
> ### ** Examples
> 
> data("example_data",package = "LinTInd")
> scarinfo<-FindIndel(data=data,scarfull=ref,scar=cutsite,indel.coverage="All",type="test",cln=8)
Error in .check_ncores(length(names)) : 8 simultaneous processes spawned
Calls: FindIndel -> makeCluster -> makePSOCKcluster -> .check_ncores
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 ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package inputenc Error: Unicode character ; (U+FF1B)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode character ; (U+FF1B)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
* checking PDF version of manual without hyperrefs or index ... ERROR
* DONE

Status: 2 ERRORs, 6 WARNINGs, 1 NOTE
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2468/5b6bced7f2c5c43821ab9b34dfa6c7c3d1ebdb73/LinTInd.Rcheck/00check.log’
for details.





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 BiocCheck('LinTInd_0.99.1.tar.gz')

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This is BiocCheck version 1.31.23. 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 19 object(s) are initialized. Maybe
      they are part of a data set loaded with data(), or perhaps part
      of an object referenced in with() or within().
    function (object)
      BuildTree (write.csv)
      change_form_stat  (scarref)
      change_form_stat (scarref)
      FindIndel  (is)
      FindIndel (write.table)
      IndelForm (write.csv)
      IndelIdents (write.csv)
      IndelIdents  (is)
      IndelPlot (Site)
      IndelPlot (Freq)
      PlotTree (tags)
      PlotTree (celltype)
      PlotTree (Freq)
      PlotTree  (tag_number)
      PlotTree (y)
      PlotTree (variable)
      PlotTree (value)
      ReadFasta (read.table)
      TagProcess (i)
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
    * NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
      removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
    * NOTE: Update R version dependency from 4.0 to 4.2.0.
* 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:
      Sequencing
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...
* 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...
    * NOTE: License '`use_mit_license()`, `use_gpl3_license()` or
      friends to pick a license' unknown; licenses cannot restrict use
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
    * NOTE: 'sessionInfo' not found in vignette(s)
      Missing from file(s):
        vignettes/tutorial.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of LinTInd...
    * WARNING: Avoid the use of 'library' or 'require' in R code
      Found in files:
        library() in R/function.R (line 243, column 19)
        library() in R/function.R (line 508, column 19)
        library() in R/function.R (line 509, column 19)
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
      Found in files:
        R/function.R (line 258, column 27)
        R/function.R (line 522, column 23)
        R/function.R (line 651, column 16)
        R/function.R (line 679, column 12)
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        R/function.R (line 1079, column 16)
        R/function.R (line 1080, column 16)
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
      Found in files:
        function.R (line 51, column 37)
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      Found in files:
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* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: Recommended function length <= 50 lines.
      There are 8 functions > 50 lines.
      The longest 5 functions are:
        PlotTree() (R/function.R, line 755): 197 lines
        IndelIdents() (R/function.R, line 381): 175 lines
        FindIndel() (R/function.R, line 184): 87 lines
        BuildTree() (R/function.R, line 638): 87 lines
        max_reads_stat() (R/function.R, line 424): 83 lines
* 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; 167 lines (10%) are > 80 characters
      long.
    First 6 lines:
      R/function.R:22 #' @description Function to create a reference datafram...
      R/function.R:25 #' @param reftype Choose the reference type you want, i...
      R/function.R:74 #' @importFrom Biostrings DNAString pairwiseAlignment n...
      R/function.R:77 #' align_to_range(p="AAGG---AAATTTCGGAATAAGGAATTT",s="A...
      R/function.R:164 #' @description This function can ident indels for eac...
      R/function.R:168 #' @param align_score The minimum alignment score that...
    * NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain
      tabs.
    First 1 lines:
      R/function.R:1007   #	return(length(which(dat==i))/length(INDEL_ranges))
    * NOTE: Consider multiples of 4 spaces for line indents, 535
      lines(31%) are not.
    First 6 lines:
      R/function.R:15   sv = read.table(filename)
      R/function.R:16   scarfull = DNAString(sv[2,1])
      R/function.R:17   return(c("scarfull" = scarfull))
      R/function.R:36   colnames(segref) = c("indx","start","end")
      R/function.R:37   scar = NULL
      R/function.R:38   type = NULL
    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.
    * ERROR: Maintainer must add package name to Watched Tags on the
      support site; Edit your Support Site User Profile to add Watched
      Tags.


Summary:
ERROR count: 1
WARNING count: 1
NOTE count: 14
For detailed information about these checks, see the BiocCheck
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https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.

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

 R CMD BUILD

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

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir LinTInd_0.99.1.tar.gz'
>>>>>>> 

* installing *source* package ‘LinTInd’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
[1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead."
[1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead."
[1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead."
[1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead."
[1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead."
[1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead."
[1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead."
[1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead."
[1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead."
[1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead."
[1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead."
[1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead."
[1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead."
[1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead."
[1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead."
[1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead."
[1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead."
[1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead."
[1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead."
[1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead."
[1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead."
[1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead."
** 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 (LinTInd)