Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘sciCNV/DESCRIPTION’ ... OK
* preparing ‘sciCNV’:
* 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
WARNING: directory ‘sciCNV/sciCNV’ is empty
* building ‘sciCNV_0.99.28.tar.gz’

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 BiocCheckGitClone('sciCNV')

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This is BiocCheckGitClone version 1.31.14. 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




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 R CMD CHECK

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* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2383/7ab11c71b8567690ebd351092174c214514de95e/sciCNV.Rcheck’
* using R Under development (unstable) (2021-11-01 r81125)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sciCNV/DESCRIPTION’ ... OK
* this is package ‘sciCNV’ version ‘0.99.28’
* 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 serialization versions ... OK
* checking whether package ‘sciCNV’ can be installed ... [4s/4s] 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
Invalid license file pointers: LICENSE
* 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 ... [7s/8s] NOTE
CNV_htmp_glist: no visible global function definition for
  ‘colorRampPalette’
CNV_htmp_gloc: no visible binding for global variable ‘genLoc1’
CNV_htmp_gloc: no visible global function definition for
  ‘colorRampPalette’
heatmap_break_gloc: no visible binding for global variable ‘genLoc1’
Undefined global functions or variables:
  colorRampPalette genLoc1
Consider adding
  importFrom("grDevices", "colorRampPalette")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'CNV_htmp_glist.Rd':
  \examples lines wider than 100 characters:
     breakGlist <- c(1,1003,1713,2289,2635,3057,3546,4024,4374,4767,5134,5707,6251,6404,6777,7093,7549,8155,8289,9006,9264,9374,9976,9976)

Rd file 'CNV_htmp_gloc.Rd':
  \examples lines wider than 100 characters:
     breakGloc <- c(1,1003,1713,2289,2635,3057,3546,4024,4374,4767,5134,5707,6251,6404,6777,7093,7549,8155,8289,9006,9264,9374,9976,9976)

Rd file 'CNV_infer.Rd':
  \examples lines wider than 100 characters:
     iCNV_percell <- CNV_infer(ss.expr=norm_expr_percell, mean.ctrl, gen.Loc, resolution=50, chr.n, P12, mat.fab)

Rd file 'Opt_MeanSD_RTAM1.Rd':
  \examples lines wider than 100 characters:
     CV_for_RTAM1 <- Opt_MeanSD_RTAM1(Normalized_log=normalized_data, Order_Matrix, nGene, Min_nGene=250, gene_cutoff=250)

Rd file 'Opt_MeanSD_RTAM2.Rd':
  \examples lines wider than 100 characters:
     CV_for_RTAM2 <- Opt_MeanSD_RTAM2(Normalized_log=normalized_data, Order_Matrix, nGene, Min_nGene=250, gene_cutoff=250)

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘10XGenomics_gen_pos_GRCh38-1.2.0’ ‘HouseKeepingGenes’
Undocumented data sets:
  ‘10XGenomics_gen_pos_GRCh38-1.2.0’ ‘HouseKeepingGenes’
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 ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'CNV_htmp_glist'
  ‘clustering.type’ ‘sorting’ ‘CNVscore’ ‘cluster.lines’ ‘breakGlist’
  ‘No.test’
Documented arguments not in \usage in documentation object 'CNV_htmp_glist':
  ‘clustering.type:’ ‘sorting:’ ‘CNVscore:’ ‘cluster.lines:’
  ‘breakGlist:’ ‘No.test:’ ‘Gen.Loc’

Undocumented arguments in documentation object 'CNV_infer'
  ‘gen.Loc’

Undocumented arguments in documentation object 'CNV_score'
  ‘M_nf’
Documented arguments not in \usage in documentation object 'CNV_score':
  ‘M_nF’

Undocumented arguments in documentation object 'RTAM_normalization'
  ‘method’ ‘Min_nGn’ ‘Optimizing’
Documented arguments not in \usage in documentation object 'RTAM_normalization':
  ‘Genes’ ‘Order_Matrix’ ‘MinNumGenes’ ‘OptNumGenes’

Undocumented arguments in documentation object 'Scaling_CNV'
  ‘n.TestCells’ ‘scaling.factor’
Documented arguments not in \usage in documentation object 'Scaling_CNV':
  ‘Vn.TestCells’ ‘Vscaling.factor’

Undocumented arguments in documentation object 'Sketch_AveCNV'
  ‘Assoc.Chr’

Undocumented arguments in documentation object 'heatmap.3'
  ‘x’ ‘Rowv’ ‘Colv’ ‘distfun’ ‘hclustfun’ ‘dendrogram’ ‘symm’ ‘scale’
  ‘na.rm’ ‘revC’ ‘add.expr’ ‘breaks’ ‘symbreaks’ ‘col’ ‘colsep’
  ‘rowsep’ ‘sepcolor’ ‘sepwidth’ ‘cellnote’ ‘notecex’ ‘notecol’
  ‘na.color’ ‘trace’ ‘tracecol’ ‘hline’ ‘vline’ ‘linecol’ ‘margins’
  ‘ColSideColors’ ‘RowSideColors’ ‘side.height.fraction’ ‘cexRow’
  ‘cexCol’ ‘labRow’ ‘labCol’ ‘key’ ‘keysize’ ‘density.info’ ‘denscol’
  ‘symkey’ ‘densadj’ ‘main’ ‘xlab’ ‘ylab’ ‘lmat’ ‘lhei’ ‘lwid’
  ‘ColSideColorsSize’ ‘RowSideColorsSize’ ‘KeyValueName’ ‘...’

Undocumented arguments in documentation object 'sciCNV'
  ‘norm.mat’ ‘ave.ctrl’ ‘gen.Loc’ ‘No.test’ ‘sharpness’ ‘baseline_adj’
  ‘baseline’
Documented arguments not in \usage in documentation object 'sciCNV':
  ‘norm.mat:’ ‘ave.ctrl:’ ‘gen.Loc:’ ‘No.test:’ ‘sharpness:’
  ‘baseline_adj:’ ‘baseline:’

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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [0s/0s] ERROR
Running examples in ‘sciCNV-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CNV_htmp_glist
> ### Title: CNV_htmp_glist function
> ### Aliases: CNV_htmp_glist
> 
> ### ** Examples
> 
> CNV.mat <- read.csv(file.choose(), header=TRUE)
Enter file name: breakGlist <- c(1,1003,1713,2289,2635,3057,3546,4024,4374,4767,5134,5707,6251,6404,6777,7093,7549,8155,8289,9006,9264,9374,9976,9976)
Warning in file(file, "rt") :
  cannot open file 'breakGlist <- c(1,1003,1713,2289,2635,3057,3546,4024,4374,4767,5134,5707,6251,6404,6777,7093,7549,8155,8289,9006,9264,9374,9976,9976)': No such file or directory
Error in file(file, "rt") : cannot open the connection
Calls: read.csv -> read.table -> file
Execution halted
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘beanplot’
'library' or 'require' calls not declared from:
  ‘Matrix’ ‘RColorBrewer’ ‘Rtsne’ ‘Seurat’ ‘beanplot’ ‘devtools’
  ‘dplyr’ ‘ggplot2’ ‘ggridges’ ‘qlcMatrix’ ‘reticulate’ ‘svd’ ‘umap’
  ‘viridis’
* 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/2383/7ab11c71b8567690ebd351092174c214514de95e/sciCNV.Rcheck/00check.log’
for details.





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 BiocCheck('sciCNV_0.99.28.tar.gz')

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This is BiocCheck version 1.31.14. 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 4 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)
      CNV_htmp_glist (colorRampPalette)
      CNV_htmp_gloc (genLoc1)
      CNV_htmp_gloc (colorRampPalette)
      heatmap_break_gloc (genLoc1)
* 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...
* Checking package size...
    * ERROR: Package Source tarball exceeds Bioconductor size
      requirement.
        Package Size: 7.0833 MB
        Size Requirement: 5.0000 MB
* 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...
    * 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 DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
    * NOTE: 'sessionInfo' not found in vignette(s)
      Missing from file(s):
        vignettes/Introduction.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of sciCNV...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
      Found in files:
        R/heatmap.3.R (line 65, column 18)
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
      Found in files:
        CNV_htmp_glist.R (line 87, column 41)
        CNV_htmp_glist.R (line 96, column 41)
        CNV_htmp_glist.R (line 102, column 41)
        CNV_htmp_glist.R (line 112, column 94)
        CNV_htmp_glist.R (line 113, column 119)
        CNV_htmp_glist.R (line 127, column 13)
        CNV_htmp_glist.R (line 128, column 14)
        CNV_htmp_glist.R (line 161, column 12)
        CNV_htmp_glist.R (line 182, column 45)
        CNV_htmp_glist.R (line 185, column 12)
        CNV_htmp_gloc.R (line 90, column 41)
        CNV_htmp_gloc.R (line 99, column 41)
        CNV_htmp_gloc.R (line 105, column 41)
        CNV_htmp_gloc.R (line 115, column 92)
        CNV_htmp_gloc.R (line 131, column 13)
        CNV_htmp_gloc.R (line 132, column 14)
        CNV_htmp_gloc.R (line 171, column 12)
        CNV_htmp_gloc.R (line 189, column 32)
        CNV_htmp_gloc.R (line 189, column 45)
        CNV_htmp_gloc.R (line 195, column 42)
        CNV_htmp_gloc.R (line 195, column 55)
        CNV_htmp_gloc.R (line 200, column 12)
        CNV_htmp_gloc.R (line 202, column 15)
        CNV_htmp_gloc.R (line 207, column 12)
        CNV_htmp_gloc.R (line 219, column 12)
        CNV_htmp_gloc.R (line 220, column 14)
        CNV_htmp_gloc.R (line 221, column 17)
        CNV_htmp_gloc.R (line 235, column 45)
        CNV_htmp_gloc.R (line 249, column 15)
        CNV_htmp_gloc.R (line 254, column 42)
        CNV_htmp_gloc.R (line 267, column 15)
        CNV_htmp_gloc.R (line 272, column 42)
        CNV_htmp_gloc.R (line 288, column 12)
        CNV_htmp_gloc.R (line 299, column 40)
        CNV_htmp_gloc.R (line 307, column 38)
        CNV_htmp_gloc.R (line 327, column 12)
        CNV_htmp_gloc.R (line 346, column 45)
        CNV_htmp_gloc.R (line 349, column 12)
        CNV_infer.R (line 84, column 13)
        CNV_infer.R (line 105, column 12)
        CNV_infer.R (line 166, column 12)
        CNV_infer.R (line 229, column 12)
        CNV_score.R (line 36, column 13)
        CNV_score.R (line 37, column 14)
        CNV_score.R (line 55, column 12)
        CNV_score.R (line 56, column 14)
        CNV_score.R (line 66, column 9)
        CNV_score.R (line 66, column 79)
        CNV_score.R (line 68, column 40)
        heatmap_break_glist.R (line 30, column 12)
        heatmap_break_gloc.R (line 33, column 12)
        heatmap_break_gloc.R (line 51, column 32)
        heatmap_break_gloc.R (line 51, column 45)
        heatmap_break_gloc.R (line 56, column 42)
        heatmap_break_gloc.R (line 56, column 55)
        heatmap_break_gloc.R (line 61, column 12)
        heatmap_break_gloc.R (line 63, column 16)
        heatmap_break_gloc.R (line 73, column 38)
        heatmap_break_gloc.R (line 73, column 57)
        heatmap.3.R (line 183, column 15)
        heatmap.3.R (line 193, column 8)
        heatmap.3.R (line 198, column 8)
        heatmap.3.R (line 276, column 19)
        heatmap.3.R (line 300, column 19)
        heatmap.3.R (line 330, column 14)
        heatmap.3.R (line 331, column 9)
        heatmap.3.R (line 331, column 15)
        heatmap.3.R (line 341, column 11)
        heatmap.3.R (line 341, column 17)
        heatmap.3.R (line 344, column 11)
        heatmap.3.R (line 371, column 13)
        Mito_umi_gn.R (line 55, column 52)
        Mito_umi_gn.R (line 63, column 42)
        Mito_umi_gn.R (line 83, column 39)
        Mito_umi_gn.R (line 83, column 71)
        Mito_umi_gn.R (line 93, column 44)
        Mito_umi_gn.R (line 101, column 44)
        Opt_MeanSD_RTAM1.R (line 41, column 12)
        Opt_MeanSD_RTAM1.R (line 46, column 14)
        Opt_MeanSD_RTAM1.R (line 65, column 13)
        Opt_MeanSD_RTAM1.R (line 68, column 14)
        Opt_MeanSD_RTAM1.R (line 118, column 12)
        Opt_MeanSD_RTAM1.R (line 128, column 12)
        Opt_MeanSD_RTAM1.R (line 129, column 14)
        Opt_MeanSD_RTAM1.R (line 137, column 12)
        Opt_MeanSD_RTAM1.R (line 147, column 12)
        Opt_MeanSD_RTAM2.R (line 44, column 12)
        Opt_MeanSD_RTAM2.R (line 49, column 14)
        Opt_MeanSD_RTAM2.R (line 64, column 12)
        Opt_MeanSD_RTAM2.R (line 69, column 14)
        Opt_MeanSD_RTAM2.R (line 82, column 12)
        Opt_MeanSD_RTAM2.R (line 87, column 14)
        Opt_MeanSD_RTAM2.R (line 111, column 12)
        Opt_MeanSD_RTAM2.R (line 113, column 15)
        Opt_MeanSD_RTAM2.R (line 122, column 12)
        Opt_MeanSD_RTAM2.R (line 123, column 14)
        Opt_MeanSD_RTAM2.R (line 132, column 12)
        Opt_MeanSD_RTAM2.R (line 142, column 12)
        RTAM_normalization.R (line 78, column 12)
        RTAM_normalization.R (line 89, column 12)
        RTAM_normalization.R (line 93, column 14)
        RTAM_normalization.R (line 105, column 12)
        RTAM_normalization.R (line 140, column 14)
        RTAM_normalization.R (line 143, column 16)
        RTAM_normalization.R (line 155, column 15)
        RTAM_normalization.R (line 158, column 16)
        RTAM_normalization.R (line 189, column 22)
        RTAM_normalization.R (line 189, column 60)
        RTAM_normalization.R (line 200, column 22)
        RTAM_normalization.R (line 200, column 60)
        RTAM_normalization.R (line 241, column 14)
        RTAM_normalization.R (line 243, column 17)
        RTAM_normalization.R (line 252, column 14)
        RTAM_normalization.R (line 253, column 16)
        RTAM_normalization.R (line 264, column 14)
        RTAM_normalization.R (line 303, column 14)
        RTAM_normalization.R (line 309, column 14)
        RTAM_normalization.R (line 310, column 16)
        RTAM_normalization.R (line 327, column 12)
        Scaling_CNV.R (line 50, column 12)
        Scaling_CNV.R (line 76, column 14)
        sciCNV.R (line 154, column 34)
        Sketch_AveCNV.R (line 41, column 12)
    * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE (found 2
      times)
        F in R/heatmap.3.R (line 279, column 43)
        F in R/heatmap.3.R (line 303, column 42)
    * WARNING: Avoid class membership checks with class() / is() and ==
      / !=; Use is(x, 'class') for S4 classes
      Found in files:
        heatmap.3.R (line 229, column 18)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths    * NOTE: Recommended function length <= 50 lines.
      There are 13 functions > 50 lines.
      The longest 5 functions are:
        heatmap.3() (R/heatmap.3.R, line 11): 449 lines
        CNV_htmp_gloc() (R/CNV_htmp_gloc.R, line 39): 397 lines
        RTAM_normalization() (R/RTAM_normalization.R, line 25): 314
      lines
        CNV_htmp_glist() (R/CNV_htmp_glist.R, line 36): 243 lines
        CNV_infer() (R/CNV_infer.R, line 32): 215 lines
* Checking man page documentation...
    * NOTE: Consider adding runnable examples to the following man
      pages which document exported objects:
      heatmap.3.Rd
* 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; 338 lines (9%) are > 80 characters
      long.
    First 6 lines:
      R/CNV_htmp_glist.R:5 #' @description Generates a heatmap of single cell...
      R/CNV_htmp_glist.R:8 #' @param Gen.Loc Genomic Location matrix with lis...
      R/CNV_htmp_glist.R:9 #' @param clustering a TRUE/FALSE variable specify...
      R/CNV_htmp_glist.R:10 #' @param clustering.type: variable specifying th...
      R/CNV_htmp_glist.R:11 #'        "euclidean", " spearman", ... "original...
      R/CNV_htmp_glist.R:12 #'         Default is "pearson". However this is ...
    * NOTE: Consider multiples of 4 spaces for line indents, 1526
      lines(39%) are not.
    First 6 lines:
      R/CNV_htmp_glist.R:37                            clustering = FALSE,   ...
      R/CNV_htmp_glist.R:38                            clustering.type = c("p...
      R/CNV_htmp_glist.R:39                            sorting = FALSE,      ...
      R/CNV_htmp_glist.R:40                            CNVscore = NULL,      ...
      R/CNV_htmp_glist.R:41                            cluster.lines = NULL,
      R/CNV_htmp_glist.R:42                            breakGlist,     # sepa...
    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: 3
WARNING count: 2
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 sciCNV_0.99.28.tar.gz'
>>>>>>> 

* installing *source* package ‘sciCNV’ ...
** 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 (sciCNV)