Bioconductor Single Package Builder - Build History

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

 R CMD BUILD

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

* checking for file ‘STdeconvolve/DESCRIPTION’ ... OK
* preparing ‘STdeconvolve’:
* 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 ‘STdeconvolve_0.99.0.tar.gz’

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

 BiocCheckGitClone('STdeconvolve')

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

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/2530/STdeconvolve_20220225132431/STdeconvolve.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 ‘STdeconvolve/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘STdeconvolve’ version ‘0.99.0’
* 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 ‘STdeconvolve’ can be installed ... [13s/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 ... NOTE
'LinkingTo' field is unused: package has no 'src' directory
* 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘KernSmooth’ ‘dplyr’ ‘gridExtra’ ‘parallel’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [17s/20s] NOTE
cleanCounts: no visible global function definition for ‘par’
cleanCounts: no visible global function definition for ‘hist’
clusterTopics: no visible global function definition for ‘as.dist’
clusterTopics: no visible global function definition for ‘cor’
clusterTopics: no visible global function definition for ‘hclust’
clusterTopics: no visible global function definition for ‘heatmap’
clusterTopics: no visible global function definition for
  ‘as.dendrogram’
correlationPlot: no visible binding for global variable ‘Var1’
correlationPlot: no visible binding for global variable ‘Var2’
correlationPlot: no visible binding for global variable ‘value’
darken: no visible global function definition for ‘col2rgb’
darken: no visible global function definition for ‘rgb’
fac2col: no visible global function definition for ‘rainbow’
fitLDA: no visible binding for global variable ‘slot’
fitLDA: no visible binding for global variable ‘rareCtsAdj’
fitLDA: no visible binding for global variable ‘K’
fitLDA: no visible binding for global variable ‘perplexAdj’
fitLDA: no visible binding for global variable ‘alphaBool’
getCorrMtx : <anonymous> : <anonymous>: no visible global function
  definition for ‘cor’
getOverdispersedGenes: no visible binding for global variable ‘var’
getOverdispersedGenes: no visible global function definition for ‘lm’
getOverdispersedGenes: no visible global function definition for
  ‘as.formula’
getOverdispersedGenes: no visible global function definition for
  ‘resid’
getOverdispersedGenes: no visible global function definition for ‘pf’
getOverdispersedGenes: no visible global function definition for
  ‘qchisq’
getOverdispersedGenes: no visible global function definition for ‘par’
getOverdispersedGenes: no visible global function definition for
  ‘smoothScatter’
getOverdispersedGenes: no visible global function definition for
  ‘lines’
getOverdispersedGenes: no visible global function definition for
  ‘predict’
getOverdispersedGenes: no visible global function definition for
  ‘points’
getOverdispersedGenes: no visible global function definition for
  ‘abline’
gg_color_hue: no visible global function definition for ‘hcl’
lighten: no visible global function definition for ‘col2rgb’
lighten: no visible global function definition for ‘rgb’
optimalModel: no visible binding for global variable ‘slot’
perplexityPlot: no visible binding for global variable ‘slot’
perplexityPlot: no visible binding for global variable ‘rareCtsAdj’
perplexityPlot: no visible binding for global variable ‘K’
perplexityPlot: no visible binding for global variable ‘perplexAdj’
perplexityPlot: no visible binding for global variable ‘alphaBool’
preprocess: no visible global function definition for ‘read.table’
preprocess: no visible global function definition for ‘par’
restrictCorpus: no visible global function definition for ‘par’
restrictCorpus: no visible global function definition for ‘hist’
transparentCol: no visible global function definition for ‘col2rgb’
transparentCol: no visible global function definition for ‘rgb’
vizAllTopics: no visible global function definition for ‘rainbow’
vizAllTopics: no visible binding for global variable ‘x’
vizAllTopics: no visible binding for global variable ‘y’
vizAllTopics: no visible binding for global variable ‘Row.names’
vizAllTopics: no visible binding for global variable ‘Pixel.Groups’
vizGeneCounts: no visible binding for global variable ‘x’
vizGeneCounts: no visible binding for global variable ‘y’
vizTopic: no visible binding for global variable ‘x’
vizTopic: no visible binding for global variable ‘y’
vizTopicClusters: no visible binding for global variable ‘x’
vizTopicClusters: no visible binding for global variable ‘y’
vizTopicClusters: no visible binding for global variable ‘Row.names’
winsorize: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  K Pixel.Groups Row.names Var1 Var2 abline alphaBool as.dendrogram
  as.dist as.formula col2rgb cor hcl hclust heatmap hist lines lm par
  perplexAdj pf points predict qchisq quantile rainbow rareCtsAdj
  read.table resid rgb slot smoothScatter value var x y
Consider adding
  importFrom("grDevices", "col2rgb", "hcl", "rainbow", "rgb")
  importFrom("graphics", "abline", "hist", "lines", "par", "points",
             "smoothScatter")
  importFrom("methods", "slot")
  importFrom("stats", "as.dendrogram", "as.dist", "as.formula", "cor",
             "hclust", "heatmap", "lm", "pf", "predict", "qchisq",
             "quantile", "resid", "var")
  importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [3s/3s]
 [4s/4s] 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: 3 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2530/STdeconvolve_20220225132431/STdeconvolve.Rcheck/00check.log’
for details.






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

 BiocCheck('STdeconvolve_0.99.0.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/2530/STdeconvolve_20220225132431/STdeconvolve_0.99.0.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpHKWSBK/file15cc733b3fd8b/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...
    * NOTE: Update R version dependency from 3.6 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...
    * WARNING: 'Deconvolution' is an invalid BiocViews term.
    * WARNING: 'TopicModels' is an invalid BiocViews term.
* Checking for recommended biocViews...
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...
    * WARNING: Import parallel, gridExtra, KernSmooth, dplyr in
      NAMESPACE as well as DESCRIPTION.
* Checking .Rbuildignore...
* Checking vignette directory...
    * ERROR: VignetteBuilder listed in DESCRIPTION but not found as
      VignetteEngine in any vignettes:
        rmarkdown
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of STdeconvolve...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
      Found in files:
        R/functions.R (line 549, column 37)
        R/functions.R (line 728, column 7)
        R/functions.R (line 765, column 7)
        R/functions.R (line 859, column 31)
        R/functions.R (line 861, column 31)
        R/functions.R (line 863, column 31)
        R/functions.R (line 864, column 23)
        R/functions.R (line 865, column 31)
        R/import.R (line 20, column 24)
        R/plot.R (line 713, column 26)
        R/plot.R (line 727, column 37)
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
      Found in files:
        functions.R (line 75, column 57)
        functions.R (line 245, column 83)
        functions.R (line 330, column 59)
        functions.R (line 513, column 17)
        functions.R (line 727, column 37)
        functions.R (line 728, column 14)
        functions.R (line 754, column 37)
        functions.R (line 765, column 14)
        functions.R (line 999, column 38)
        import.R (line 208, column 25)
        plot.R (line 589, column 34)
        plot.R (line 716, column 17)
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
      Found in files:
        cat() in R/functions.R (line 774, column 21)
        print() in R/functions.R (line 354, column 3)
        print() in R/functions.R (line 615, column 5)
        cat() in R/misc.R (line 387, column 9)
        print() in R/misc.R (line 330, column 5)
        print() in R/plot.R (line 320, column 5)
        print() in R/plot.R (line 779, column 3)
    * NOTE: Avoid using '=' for assignment and use '<-' instead
      Found in files:
        R/import.R (line 140, column 35)
        R/misc.R (line 29, column 20)
        R/misc.R (line 30, column 12)
        R/misc.R (line 32, column 20)
        R/misc.R (line 33, column 12)
        R/misc.R (line 35, column 20)
        R/misc.R (line 36, column 12)
        R/misc.R (line 38, column 20)
        R/misc.R (line 39, column 12)
        R/misc.R (line 41, column 20)
        R/misc.R (line 42, column 12)
        R/plot.R (line 588, column 8)
    * NOTE: Avoid the use of 'paste' in condition signals
      Found in files:
        R/functions.R (line 32, column 13)
        R/functions.R (line 37, column 13)
        R/functions.R (line 43, column 13)
        R/functions.R (line 48, column 13)
        R/functions.R (line 53, column 13)
        R/import.R (line 149, column 15)
        R/import.R (line 167, column 13)
        R/import.R (line 286, column 13)
    * NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
      Found in files:
        R/functions.R (line 234, column 15)
        R/functions.R (line 279, column 15)
        R/functions.R (line 299, column 15)
        R/functions.R (line 774, column 25)
    * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE (found 3
      times)
        T in R/import.R (line 157, column 69)
        F in R/import.R (line 157, column 61)
        F in R/import.R (line 199, column 77)
    * WARNING: Remove set.seed usage (found 2 times)
        set.seed() in R/functions.R (line 433, column 5)
        set.seed() in R/functions.R (line 439, column 5)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: Recommended function length <= 50 lines.
      There are 15 functions > 50 lines.
      The longest 5 functions are:
        buildBregmaCorpus() (R/misc.R, line 438): 238 lines
        preprocess() (R/functions.R, line 156): 222 lines
        fitLDA() (R/functions.R, line 413): 215 lines
        vizTopicClusters() (R/plot.R, line 175): 156 lines
        vizAllTopics() (R/plot.R, line 26): 117 lines
* Checking man page documentation...
    * WARNING: Add non-empty \value sections to the following man
      pages: man/bh.adjust.Rd, man/correlationPlot_2.Rd,
      man/correlationPlot.Rd, man/darken.Rd, man/gg_color_hue.Rd,
      man/lighten.Rd, man/perplexityPlot.Rd, man/restrictCorpus.Rd,
      man/transparentCol.Rd, man/vizAllTopics.Rd, man/vizGeneCounts.Rd,
      man/vizTopic.Rd, man/vizTopicClusters.Rd
    * ERROR: At least 80% of man pages documenting exported objects
      must have runnable examples. The following pages do not:
      annotateCellTypesGSEA.Rd, bh.adjust.Rd, cleanCounts.Rd,
  correlationPlot.Rd, darken.Rd, filterTheta.Rd, fitLDA.Rd,
  getBetaTheta.Rd, getCorrMtx.Rd, getOverdispersedGenes.Rd,
  gg_color_hue.Rd, lighten.Rd, lsatPairs.Rd, normalizeCounts.Rd,
  optimalModel.Rd, perplexityPlot.Rd, preprocess.Rd, reduceTheta.Rd,
  restrictCorpus.Rd, scale0_1.Rd, topGenes.Rd, transparentCol.Rd,
  vizAllTopics.Rd, vizGeneCounts.Rd, vizTopic.Rd, where.is.knee.Rd,
  winsorize.Rd
* Checking package NEWS...
* 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; 475 lines (11%) are > 80 characters
      long.
    First 6 lines:
      R/data.R:3 #' @format List where 'counts' is a sparse matrix with colum...
      R/data.R:13 # @format List where 'mat' is a sparse matrix with columns ...
      R/data.R:14 #                          where expression values have alr...
      R/data.R:16 #                          and brain position as 6 slice in...
      R/data.R:23 #' @format List where 'counts' is a sparse matrix with colu...
      R/functions.R:3 #' @description identifies over dispersed genes across ...
    * NOTE: Consider multiples of 4 spaces for line indents, 1356
      lines(31%) are not.
    First 6 lines:
      R/functions.R:22                            removeAbove=1.0,
      R/functions.R:23                            removeBelow=0.05,
      R/functions.R:24                            alpha=0.05,
      R/functions.R:25                            nTopOD=1000,
      R/functions.R:26                            plot=FALSE,
      R/functions.R:27                            verbose=TRUE) {
    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...
    * ERROR: Maintainer must subscribe to the bioc-devel mailing list.
      Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
    * ERROR: Maintainer must register at the support site; visit
      https://support.bioconductor.org/accounts/signup/ .


Summary:
ERROR count: 4
WARNING count: 6
NOTE count: 11
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
BiocCheck FAILED.

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

 R CMD BUILD

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

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir STdeconvolve_0.99.0.tar.gz'
>>>>>>> 

* installing *source* package ‘STdeconvolve’ ...
** using staged installation
** R
** data
** 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 (STdeconvolve)