Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘PanViz/DESCRIPTION’ ... OK
* preparing ‘PanViz’:
* 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 ‘PanViz_0.99.2.tar.gz’

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 BiocCheckGitClone('PanViz')

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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




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 R CMD CHECK

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* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2505/fcb81682b5cfec01dcb117c9f9d4eca046f6508c/PanViz.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 ‘PanViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PanViz’ version ‘0.99.2’
* 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 ‘PanViz’ 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 ... OK
* 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 ... [6s/6s] NOTE
GWAS_data_reader: no visible global function definition for ‘all_of’
colour_IMON: no visible global function definition for ‘from’
Undefined global functions or variables:
  all_of from
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'GWAS_data_reader.Rd':
  \examples lines wider than 100 characters:
     path = system.file("extdata", "gwas-association-downloaded_2021-09-13-EFO_1000649.tsv", package="PanViz")
     df <- PanViz::GWAS_data_reader(file = path, snp_col = "SNPS", study_col = "STUDY", trait_col = "DISEASE/TRAIT")
     df <- PanViz::GWAS_data_reader(file = path, snp_col = "Source Marker Accession", study_col = "Study Name", trait_col = "Annotation Name ... [TRUNCATED]

Rd file 'get_grouped_IMON.Rd':
  \examples lines wider than 100 characters:
     ##getting GWAS Catalog association tsv file and cleaning up using GWAS_catalog_tsv_to_dataframe function:
     df <- PanViz::GWAS_data_reader(file = system.file("extdata", "gwas-association-downloaded_2021-09-13-EFO_1000649.tsv", package="PanViz" ... [TRUNCATED]
     G <- PanViz::get_grouped_IMON(dataframe = df, groupby = "studies", ego = 5, save_file = FALSE, colour_groups = FALSE)
     G <- PanViz::get_grouped_IMON(dataframe = df, groupby = "studies", ego = 5, save_file = FALSE, colour_groups = TRUE)

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 R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [94s/99s] OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
get_grouped_IMON 83.582  0.364  86.274
decompose_IMON    6.904  0.291   8.532
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [100s/107s]
 [100s/107s] 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: 2 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2505/fcb81682b5cfec01dcb117c9f9d4eca046f6508c/PanViz.Rcheck/00check.log’
for details.






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 BiocCheck('PanViz_0.99.2.tar.gz')

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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/2505/fcb81682b5cfec01dcb117c9f9d4eca046f6508c/PanViz_0.99.2.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmptcbLy5/file1536216a72cec/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 4.1.0 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...
* 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...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of PanViz...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
      Found in files:
        R/get_grouped_IMON.R (line 28, column 31)
        R/get_IMON.R (line 21, column 31)
        R/NCBI_gene_locations.R (line 24, column 25)
        R/Reactions_Get_All.R (line 46, column 27)
        R/Reactions_Get_All.R (line 52, column 26)
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
      Found in files:
        adjl_to_G_grouped.R (line 122, column 21)
        Genes_Get_All.R (line 27, column 44)
        get_compound_hashmap.R (line 24, column 47)
        NCBI_gene_locations.R (line 14, column 12)
        Reactions_Get_All.R (line 26, column 47)
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
      Found in files:
        cat() in R/adjl_to_G_grouped.R (line 19, column 3)
        cat() in R/adjl_to_G_grouped.R (line 67, column 3)
        cat() in R/adjl_to_G.R (line 14, column 3)
        cat() in R/adjl_to_G.R (line 61, column 3)
        cat() in R/colour_IMON.R (line 74, column 3)
        cat() in R/colour_IMON.R (line 116, column 3)
        cat() in R/Genes_Get_All.R (line 12, column 3)
        cat() in R/Genes_Get_All.R (line 47, column 3)
        cat() in R/Genes_Get_All.R (line 48, column 3)
        cat() in R/get_grouped_IMON.R (line 138, column 3)
        cat() in R/get_grouped_IMON.R (line 160, column 5)
        cat() in R/get_grouped_IMON.R (line 163, column 5)
        cat() in R/get_IMON.R (line 87, column 3)
        cat() in R/get_IMON.R (line 113, column 5)
        cat() in R/get_IMON.R (line 116, column 5)
        cat() in R/Get_Kegg_Data.R (line 25, column 3)
        cat() in R/NCBI_dbSNP_query.R (line 11, column 3)
        cat() in R/NCBI_gene_locations.R (line 10, column 3)
        cat() in R/Reactions_Get_All.R (line 10, column 3)
        cat() in R/Reactions_Get_All.R (line 54, column 3)
        cat() in R/Reactions_Get_All.R (line 55, column 3)
    * NOTE: Avoid using '=' for assignment and use '<-' instead
      Found in files:
        R/adjl_to_G_grouped.R (line 28, column 14)
        R/adjl_to_G_grouped.R (line 122, column 19)
        R/adjl_to_G.R (line 23, column 14)
        R/adjl_to_G.R (line 74, column 53)
        R/adjl_to_G.R (line 75, column 54)
        R/adjl_to_G.R (line 77, column 54)
        R/adjl_to_G.R (line 78, column 55)
        R/adjl_to_G.R (line 80, column 65)
        R/adjl_to_G.R (line 81, column 66)
        R/dbSNP_query_clean_helper.R (line 22, column 10)
        R/decompose_IMON.R (line 20, column 5)
        R/decompose_IMON.R (line 27, column 9)
        R/decompose_IMON.R (line 33, column 5)
        R/ego_IMON.R (line 13, column 10)
        R/ego_IMON.R (line 32, column 55)
        R/ego_IMON.R (line 33, column 54)
        R/ego_IMON.R (line 35, column 56)
        R/ego_IMON.R (line 36, column 55)
        R/ego_IMON.R (line 38, column 67)
        R/ego_IMON.R (line 39, column 66)
        R/Genes_Get_All.R (line 11, column 8)
        R/Genes_Get_All.R (line 21, column 11)
        R/get_compound_hashmap.R (line 19, column 11)
        R/Reactions_Get_All.R (line 9, column 8)
        R/Reactions_Get_All.R (line 20, column 11)
        R/retry.R (line 11, column 12)
        R/retry.R (line 12, column 10)
        R/retry.R (line 14, column 14)
        R/retry.R (line 16, column 11)
        R/retry.R (line 20, column 11)
        R/retry.R (line 26, column 12)
    * NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
      Found in files:
        R/get_grouped_IMON.R (line 58, column 13)
        R/get_IMON.R (line 49, column 13)
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3
      times)
        suppressWarnings() in R/adjl_to_G_grouped.R (line 100, column
      10)
        suppressWarnings() in R/NCBI_dbSNP_query.R (line 16, column 29)
        suppressWarnings() in R/NCBI_dbSNP_query.R (line 25, column 29)
* Checking function lengths...
    * NOTE: Recommended function length <= 50 lines.
      There are 5 functions > 50 lines.
      The longest 5 functions are:
        get_grouped_IMON() (R/get_grouped_IMON.R, line 22): 145 lines
        colour_IMON() (R/colour_IMON.R, line 13): 124 lines
        adjl_to_G_grouped() (R/adjl_to_G_grouped.R, line 17): 108 lines
        get_IMON() (R/get_IMON.R, line 19): 101 lines
        adjl_to_G() (R/adjl_to_G.R, line 13): 81 lines
* Checking man page documentation...
    * NOTE: Consider adding runnable examples to the following man
      pages which document exported objects:
      Get_Kegg_Data.Rd
    * NOTE: Usage of dontrun{} / donttest{} found in man page examples.
      30% of man pages use one of these cases.
      Found in the following files:
        adjl_to_G_grouped.Rd
        adjl_to_G.Rd
        colour_IMON.Rd
        dbSNP_query_check.Rd
        ego_IMON.Rd
        gene_cleanup.Rd
        Genes_Get_All.Rd
        get_compound_hashmap.Rd
        Get_Kegg_Data.Rd
    * NOTE: Use donttest{} instead of dontrun{}.
      Found in the following files:
        adjl_to_G_grouped.Rd
        adjl_to_G.Rd
        colour_IMON.Rd
        dbSNP_query_check.Rd
        ego_IMON.Rd
        gene_cleanup.Rd
        Genes_Get_All.Rd
        get_compound_hashmap.Rd
        Get_Kegg_Data.Rd
* Checking package NEWS...
    * NOTE: Consider adding a NEWS file, so your package news will be
      included in Bioconductor release announcements.
* 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; 384 lines (16%) are > 80 characters
      long.
    First 6 lines:
      R/adjl_to_G_grouped.R:2 #' @description Internal function that construc...
      R/adjl_to_G_grouped.R:3 #' @param adjl_G_S - adjacency list containing ...
      R/adjl_to_G_grouped.R:4 #' @param unique_group_names - a list of the un...
      R/adjl_to_G_grouped.R:5 #' @param unique_group_cols - a list of unique ...
      R/adjl_to_G_grouped.R:6 #' @param group_snps - a recursive list contain...
      R/adjl_to_G_grouped.R:7 #' @param colour_groups - boolean: whether or n...
    * NOTE: Consider multiples of 4 spaces for line indents, 810
      lines(35%) are not.
    First 6 lines:
      R/adjl_to_G_grouped.R:18   ##loading KEGG network data adjacency lists ...
      R/adjl_to_G_grouped.R:19   cat("Generating IMON \n")
      R/adjl_to_G_grouped.R:20   ##creating IMON network by building up netwo...
      R/adjl_to_G_grouped.R:21   ##creating edgelist dataframe for G_S (SNP -...
      R/adjl_to_G_grouped.R:22   G_S <- utils::stack(adjl_G_S)
      R/adjl_to_G_grouped.R:23   G_S$values <- paste0("hsa: ", G_S$values) #a...
    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.
    Package name is in support site watched tags.


Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 15
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 BUILD

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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir PanViz_0.99.2.tar.gz'
>>>>>>> 

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