===============================
R CMD BUILD
===============================
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* preparing ‘ReUseData’:
* 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 ‘ReUseData_0.99.33.tar.gz’
===============================
BiocCheckGitClone('ReUseData')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: ReUseData
─ PackageVersion: 0.99.33
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2868/5e0226589c3c9ec6f63892ce65cd5304ad8e6658/ReUseData
─ 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')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2868/5e0226589c3c9ec6f63892ce65cd5304ad8e6658/ReUseData.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘0.99.33’
* 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 ‘ReUseData’ 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 ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] 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 ... NOTE
Error: package or namespace load failed for ‘ReUseData’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘BiocGenerics’
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
attr(package, "LibPath") <- which.lib.loc
ns <- loadNamespace(package, lib.loc)
env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
}, error = function(e) {
P <- if (!is.null(cc <- conditionCall(e)))
paste(" in", deparse(cc)[1L])
else ""
msg <- gettextf("package or namespace load failed for %s%s:\n %s",
sQuote(package), P, conditionMessage(e))
if (logical.return && !quietly)
message(paste("Error:", msg), domain = NA)
else stop(msg, call. = FALSE, domain = NA)
})
1: library(package, lib.loc = lib.loc, charac
Execution halted
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... [10s/10s] NOTE
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
there is no package called ‘BiocGenerics’
Calls: <Anonymous>
Execution halted
* 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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [36s/37s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dataUpdate 8.480 0.447 8.927
getCloudData 6.272 0.315 7.608
dataHub-class 5.112 0.304 5.416
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [20s/20s]
[20s/21s] 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 ... [3s/3s] OK
* DONE
Status: 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2868/5e0226589c3c9ec6f63892ce65cd5304ad8e6658/ReUseData.Rcheck/00check.log’
for details.
===============================
BiocCheck('ReUseData_0.99.33.tar.gz')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: ReUseData
─ PackageVersion: 0.99.33
─ sourceDir: /tmp/Rtmp8AgPk3/file2c8cb7ad43581/ReUseData
─ installDir: /tmp/Rtmp8AgPk3/file2c8cb736ff8c29
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2868/5e0226589c3c9ec6f63892ce65cd5304ad8e6658/ReUseData.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...
* Checking biocViews validity...
* Checking for recommended biocViews...
* NOTE: Consider adding these automatically suggested biocViews:
WorkflowManagement
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 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 ReUseData...
* Checking coding practice...
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 41 functions greater than 50 lines.
* Checking man page documentation...
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘S4Vectors’
Calls: BiocCheck ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
===============================
R CMD BUILD
===============================
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* preparing ‘ReUseData’:
* 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 ‘ReUseData_0.99.33.tar.gz’
===============================
BiocCheckGitClone('ReUseData')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: ReUseData
─ PackageVersion: 0.99.33
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2868/5e0226589c3c9ec6f63892ce65cd5304ad8e6658/ReUseData
─ 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')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2868/5e0226589c3c9ec6f63892ce65cd5304ad8e6658/ReUseData.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
Apple clang version 12.0.0 (clang-1200.0.32.29)
GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘0.99.33’
* 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 ‘ReUseData’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* 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 ... [4s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the package can be unloaded cleanly ... [4s/4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the namespace can be unloaded cleanly ... [4s/4s] OK
* checking loading without being on the library search path ... [4s/4s] 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] OK
* 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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [42s/43s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dataUpdate 11.555 1.247 12.952
getCloudData 6.187 0.366 7.120
dataHub-class 5.327 0.388 5.723
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [24s/25s]
[24s/25s] 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 ... [5s/5s] OK
* DONE
Status: 1 NOTE
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2868/5e0226589c3c9ec6f63892ce65cd5304ad8e6658/ReUseData.Rcheck/00check.log’
for details.
===============================
BiocCheck('ReUseData_0.99.33.tar.gz')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: ReUseData
─ PackageVersion: 0.99.33
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpQzpuIQ/file5a2b3dda18aa/ReUseData
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpQzpuIQ/file5a2b6a26843b
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2868/5e0226589c3c9ec6f63892ce65cd5304ad8e6658/ReUseData.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...
* Checking biocViews validity...
* Checking for recommended biocViews...
* NOTE: Consider adding these automatically suggested biocViews:
WorkflowManagement
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 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 ReUseData...
* Checking coding practice...
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 41 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 25% of man pages use at least one of these tags.
* NOTE: Use donttest{} instead of dontrun{}.
* 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; 36 lines (1%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 145 lines
(5%) are not.
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 | 0 WARNINGS | 9 NOTES
See the ReUseData.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir ReUseData_0.99.33.tar.gz'
>>>>>>>
* installing *source* package ‘ReUseData’ ...
** 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 (ReUseData)