Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘MicroBioMap/DESCRIPTION’ ... OK
* preparing ‘MicroBioMap’:
* 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 ‘MicroBioMap_0.99.8.tar.gz’

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 BiocCheckGitClone('MicroBioMap')

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─ BiocCheckVersion: 1.37.12
─ BiocVersion: 3.18
─ Package: MicroBioMap
─ PackageVersion: 0.99.8
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3100/f1fda163075c19f149dce2f0acd34a61f0bb29bc/MicroBioMap
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES

For more details, run
    browseVignettes(package = 'BiocCheck')




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 R CMD CHECK

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* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3100/f1fda163075c19f149dce2f0acd34a61f0bb29bc/MicroBioMap.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MicroBioMap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MicroBioMap’ version ‘0.99.8’
* 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 ‘MicroBioMap’ 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 ... 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 ... [6s/6s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [6s/6s] WARNING
Loading required package: TreeSummarizedExperiment
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

The following objects are masked from ‘package:matrixStats’:

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:utils’:

    findMatches

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: ‘Biobase’

The following object is masked from ‘package:MatrixGenerics’:

    rowMedians

The following objects are masked from ‘package:matrixStats’:

    anyMissing, rowMedians

Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Loading required package: ape

Attaching package: ‘ape’

The following object is masked from ‘package:Biostrings’:

    complement

Error: package or namespace load failed for ‘MicroBioMap’ in loadNamespace(package, lib.loc):
 there is no package called ‘MicroBioMap’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Error in find.package(package, lib.loc) : 
  there is no package called ‘MicroBioMap’
Execution halted
* checking S3 generic/method consistency ... WARNING
Error in find.package(package, lib.loc) : 
  there is no package called ‘MicroBioMap’
Calls: <Anonymous> -> find.package
Execution halted
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Error in find.package(package, lib.loc) : 
  there is no package called ‘MicroBioMap’
Calls: <Anonymous> -> find.package
Execution halted
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Error in find.package(package, lib.loc) : 
  there is no package called ‘MicroBioMap’
Calls: <Anonymous> -> find.package
Execution halted
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... [1s/2s] NOTE
Error in find.package(package, lib.loc) : 
  there is no package called ‘MicroBioMap’
Calls: <Anonymous> -> find.package
Execution halted
Error in loadNamespace(name) : there is no package called ‘MicroBioMap’
Calls: <Anonymous>
Execution halted
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... WARNING
Error in find.package(package, lib.loc) : 
  there is no package called ‘MicroBioMap’
Calls: <Anonymous> -> find.package
Execution halted
* checking Rd line widths ... NOTE
Error in find.package(package, lib.loc) : 
  there is no package called ‘MicroBioMap’
Calls: suppressPackageStartupMessages ... withCallingHandlers -> <Anonymous> -> Rd_db -> find.package
Execution halted
These lines will be truncated in the PDF manual.
* checking Rd cross-references ... WARNING
Warning in gzfile(file, "rb") :
  cannot open compressed file '', probable reason 'No such file or directory'
Error in gzfile(file, "rb") : cannot open the connection
Calls: <Anonymous> -> readRDS -> gzfile
Execution halted
* checking for missing documentation entries ... WARNING
Error in find.package(package, lib.loc) : 
  there is no package called ‘MicroBioMap’
Calls: <Anonymous> -> dirname -> find.package
Execution halted
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
Error in find.package(package, lib.loc) : 
  there is no package called ‘MicroBioMap’
Calls: <Anonymous> -> find.package
Execution halted
Error in find.package(package, lib.loc) : 
  there is no package called ‘MicroBioMap’
Calls: <Anonymous> -> find.package
Execution halted
Error in find.package(package, lib.loc) : 
  there is no package called ‘MicroBioMap’
Calls: <Anonymous> -> find.package
Execution halted
* checking Rd \usage sections ... WARNING
Error in find.package(package, lib.loc) : 
  there is no package called ‘MicroBioMap’
Calls: <Anonymous> -> find.package
Execution halted
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.
Error in find.package(package, lib.loc) : 
  there is no package called ‘MicroBioMap’
Calls: <Anonymous> -> find.package
Execution halted
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... WARNING
Error in find.package(package, lib.loc) : 
  there is no package called ‘MicroBioMap’
Calls: <Anonymous> -> find.package
Execution halted
* checking for unstated dependencies in examples ... WARNING
Error in find.package(package, lib.loc) : 
  there is no package called ‘MicroBioMap’
Execution halted
* checking files in ‘vignettes’ ... OK
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [0s/0s]
 [0s/1s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(MicroBioMap)
  Error in library(MicroBioMap) : there is no package called 'MicroBioMap'
  Execution halted
* checking for unstated dependencies in vignettes ... NOTE
Error in find.package(package, lib.loc) : 
  there is no package called ‘MicroBioMap’
Execution halted
* 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 ... [4s/4s] OK
* DONE

Status: 1 ERROR, 10 WARNINGs, 5 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/3100/f1fda163075c19f149dce2f0acd34a61f0bb29bc/MicroBioMap.Rcheck/00check.log’
for details.





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 BiocCheck('MicroBioMap_0.99.8.tar.gz')

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─ BiocCheckVersion: 1.37.12
─ BiocVersion: 3.18
─ Package: MicroBioMap
─ PackageVersion: 0.99.8
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpiR98ER/file4c585fdfb52f/MicroBioMap
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpiR98ER/file4c58628ca40d
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3100/f1fda163075c19f149dce2f0acd34a61f0bb29bc/MicroBioMap.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* 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...
* 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...
    * WARNING: Use biocViews from one category only (one of Software,
      ExperimentData, AnnotationData, Workflow)
Search 'biocViews' at https://contributions.bioconductor.org
* 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 for recommeded fields in DESCRIPTION...
    * NOTE: Provide 'BugReports' field(s) in DESCRIPTION
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of MicroBioMap...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
* 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; 2 lines (1%) are > 80 characters
      long.
    See https://contributions.bioconductor.org/r-code.html
    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.

─ BiocCheck results ──
0 ERRORS | 1 WARNINGS | 3 NOTES

See the MicroBioMap.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.

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 R CMD BUILD

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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir MicroBioMap_0.99.8.tar.gz'
>>>>>>> 

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