===============================
R CMD BUILD
===============================
* checking for file ‘DESpace/DESCRIPTION’ ... OK
* preparing ‘DESpace’:
* 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 ‘DESpace_0.99.0.tar.gz’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘DESpace/vignettes/DESpace_cache/html/expression plots all cluster_f3fefb3479619e95dccf17e996690983.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘DESpace/vignettes/DESpace_cache/html/expression plots all cluster_f3fefb3479619e95dccf17e996690983.rdb’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘DESpace/vignettes/DESpace_cache/html/expression plots all cluster_f3fefb3479619e95dccf17e996690983.rdx’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘DESpace/vignettes/DESpace_cache/html/expression plots high_low_bb6ec372eb19a765955e616deca49e9b.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘DESpace/vignettes/DESpace_cache/html/individual cluster test [multiple-sample]_b8d12cbdeafe85ef0b31f7542054203b.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘DESpace/vignettes/DESpace_cache/html/individual cluster test [multiple-sample]_b8d12cbdeafe85ef0b31f7542054203b.rdb’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘DESpace/vignettes/DESpace_cache/html/individual cluster test [multiple-sample]_b8d12cbdeafe85ef0b31f7542054203b.rdx’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘DESpace/vignettes/DESpace_cache/html/top SVGs expression plot [multi]_92759d511bff77f76c7ce400fe52df34.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘DESpace/vignettes/DESpace_cache/html/top SVGs expression plot [multi]_92759d511bff77f76c7ce400fe52df34.rdb’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘DESpace/vignettes/DESpace_cache/html/top SVGs expression plot [multi]_92759d511bff77f76c7ce400fe52df34.rdx’
===============================
BiocCheckGitClone('DESpace')
===============================
─ BiocCheckVersion: 1.35.12
─ BiocVersion: 3.17
─ Package: DESpace
─ PackageVersion: 0.99.0
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2946/DESpace_20230303163611/DESpace
─ 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/2946/DESpace_20230303163611/DESpace.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 ‘DESpace/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DESpace’ 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 ... WARNING
Found the following files with non-portable file names:
vignettes/DESpace_cache/html/DESpace [multi]_2dda3b9578336810ed80f107904c1444.RData
vignettes/DESpace_cache/html/DESpace [multi]_2dda3b9578336810ed80f107904c1444.rdb
vignettes/DESpace_cache/html/DESpace [multi]_2dda3b9578336810ed80f107904c1444.rdx
vignettes/DESpace_cache/html/QC genes_6d1a5904ba01b2b376baa968f7d9a8fc.RData
vignettes/DESpace_cache/html/QC genes_6d1a5904ba01b2b376baa968f7d9a8fc.rdb
vignettes/DESpace_cache/html/QC genes_6d1a5904ba01b2b376baa968f7d9a8fc.rdx
vignettes/DESpace_cache/html/QC spots_27c6e94363b78704df31febb5891e5ef.RData
vignettes/DESpace_cache/html/QC spots_27c6e94363b78704df31febb5891e5ef.rdb
vignettes/DESpace_cache/html/QC spots_27c6e94363b78704df31febb5891e5ef.rdx
vignettes/DESpace_cache/html/expression plots all cluster_f3fefb3479619e95dccf17e996690983.RData
vignettes/DESpace_cache/html/expression plots all cluster_f3fefb3479619e95dccf17e996690983.rdb
vignettes/DESpace_cache/html/expression plots all cluster_f3fefb3479619e95dccf17e996690983.rdx
vignettes/DESpace_cache/html/expression plots high_low_bb6ec372eb19a765955e616deca49e9b.RData
vignettes/DESpace_cache/html/expression plots high_low_bb6ec372eb19a765955e616deca49e9b.rdb
vignettes/DESpace_cache/html/expression plots high_low_bb6ec372eb19a765955e616deca49e9b.rdx
vignettes/DESpace_cache/html/free memory_12f5e8bc366b873142e6e39bfd02c9ec.RData
vignettes/DESpace_cache/html/free memory_12f5e8bc366b873142e6e39bfd02c9ec.rdb
vignettes/DESpace_cache/html/free memory_12f5e8bc366b873142e6e39bfd02c9ec.rdx
vignettes/DESpace_cache/html/individual cluster test [multiple-sample]_b8d12cbdeafe85ef0b31f7542054203b.RData
vignettes/DESpace_cache/html/individual cluster test [multiple-sample]_b8d12cbdeafe85ef0b31f7542054203b.rdb
vignettes/DESpace_cache/html/individual cluster test [multiple-sample]_b8d12cbdeafe85ef0b31f7542054203b.rdx
vignettes/DESpace_cache/html/individual cluster test_4490a428b98a6f11cd6aa1bf3c8e17cd.RData
vignettes/DESpace_cache/html/individual cluster test_4490a428b98a6f11cd6aa1bf3c8e17cd.rdb
vignettes/DESpace_cache/html/individual cluster test_4490a428b98a6f11cd6aa1bf3c8e17cd.rdx
vignettes/DESpace_cache/html/show top results high_e272517ee9c0228d945d70d571f9860a.RData
vignettes/DESpace_cache/html/show top results high_e272517ee9c0228d945d70d571f9860a.rdb
vignettes/DESpace_cache/html/show top results high_e272517ee9c0228d945d70d571f9860a.rdx
vignettes/DESpace_cache/html/show top results low_693387d7a90b0d5029fe6a6c7b20b110.RData
vignettes/DESpace_cache/html/show top results low_693387d7a90b0d5029fe6a6c7b20b110.rdb
vignettes/DESpace_cache/html/show top results low_693387d7a90b0d5029fe6a6c7b20b110.rdx
vignettes/DESpace_cache/html/stLearn[py multi-sample]_d23ca4ab7ec56144bef15ef0af47021c.RData
vignettes/DESpace_cache/html/stLearn[py multi-sample]_d23ca4ab7ec56144bef15ef0af47021c.rdb
vignettes/DESpace_cache/html/stLearn[py multi-sample]_d23ca4ab7ec56144bef15ef0af47021c.rdx
vignettes/DESpace_cache/html/stLearn[r multi-sample]_befaffbfd3644adf863ea2422fb491b4.RData
vignettes/DESpace_cache/html/stLearn[r multi-sample]_befaffbfd3644adf863ea2422fb491b4.rdb
vignettes/DESpace_cache/html/stLearn[r multi-sample]_befaffbfd3644adf863ea2422fb491b4.rdx
vignettes/DESpace_cache/html/top SVGs expression plot [multi]_92759d511bff77f76c7ce400fe52df34.RData
vignettes/DESpace_cache/html/top SVGs expression plot [multi]_92759d511bff77f76c7ce400fe52df34.rdb
vignettes/DESpace_cache/html/top SVGs expression plot [multi]_92759d511bff77f76c7ce400fe52df34.rdx
vignettes/DESpace_cache/html/top SVGs expression plot_d0ee96e85f73f7f6396d20bb7e451108.RData
vignettes/DESpace_cache/html/top SVGs expression plot_d0ee96e85f73f7f6396d20bb7e451108.rdb
vignettes/DESpace_cache/html/top SVGs expression plot_d0ee96e85f73f7f6396d20bb7e451108.rdx
vignettes/DESpace_cache/html/top results WM_971366c914ccfafb00f9cfd15eb885bb.RData
vignettes/DESpace_cache/html/top results WM_971366c914ccfafb00f9cfd15eb885bb.rdb
vignettes/DESpace_cache/html/top results WM_971366c914ccfafb00f9cfd15eb885bb.rdx
vignettes/DESpace_cache/html/top results all_1606fd66f6f2ee3b7abe7a2ab43c7284.RData
vignettes/DESpace_cache/html/top results all_1606fd66f6f2ee3b7abe7a2ab43c7284.rdb
vignettes/DESpace_cache/html/top results all_1606fd66f6f2ee3b7abe7a2ab43c7284.rdx
vignettes/DESpace_cache/html/top results high_low_748ffb1a285a08d90420e61b24855595.RData
vignettes/DESpace_cache/html/top results high_low_748ffb1a285a08d90420e61b24855595.rdb
vignettes/DESpace_cache/html/top results high_low_748ffb1a285a08d90420e61b24855595.rdx
vignettes/DESpace_cache/html/view LIBD layers [multi]_979a23a988921dc7d56e6d9248cb9ce3.RData
vignettes/DESpace_cache/html/view LIBD layers [multi]_979a23a988921dc7d56e6d9248cb9ce3.rdb
vignettes/DESpace_cache/html/view LIBD layers [multi]_979a23a988921dc7d56e6d9248cb9ce3.rdx
vignettes/DESpace_cache/html/view LIBD layers_840d0e47cc08aef8afa4c84108cb8e33.RData
vignettes/DESpace_cache/html/view LIBD layers_840d0e47cc08aef8afa4c84108cb8e33.rdb
vignettes/DESpace_cache/html/view LIBD layers_840d0e47cc08aef8afa4c84108cb8e33.rdx
vignettes/DESpace_cache/html/visualize colData_cdb09c1a9d3a9989156a11a4c56630a2.RData
vignettes/DESpace_cache/html/visualize colData_cdb09c1a9d3a9989156a11a4c56630a2.rdb
vignettes/DESpace_cache/html/visualize colData_cdb09c1a9d3a9989156a11a4c56630a2.rdx
vignettes/DESpace_cache/html/visualize results WM_6761dac8f875390183c6d9400f0746ff.RData
vignettes/DESpace_cache/html/visualize results WM_6761dac8f875390183c6d9400f0746ff.rdb
vignettes/DESpace_cache/html/visualize results WM_6761dac8f875390183c6d9400f0746ff.rdx
These are not fully portable file names.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Found the following non-portable file paths:
DESpace/vignettes/DESpace_cache/html/expression plots all cluster_f3fefb3479619e95dccf17e996690983.RData
DESpace/vignettes/DESpace_cache/html/expression plots all cluster_f3fefb3479619e95dccf17e996690983.rdb
DESpace/vignettes/DESpace_cache/html/expression plots all cluster_f3fefb3479619e95dccf17e996690983.rdx
DESpace/vignettes/DESpace_cache/html/expression plots high_low_bb6ec372eb19a765955e616deca49e9b.RData
DESpace/vignettes/DESpace_cache/html/individual cluster test [multiple-sample]_b8d12cbdeafe85ef0b31f7542054203b.RData
DESpace/vignettes/DESpace_cache/html/individual cluster test [multiple-sample]_b8d12cbdeafe85ef0b31f7542054203b.rdb
DESpace/vignettes/DESpace_cache/html/individual cluster test [multiple-sample]_b8d12cbdeafe85ef0b31f7542054203b.rdx
DESpace/vignettes/DESpace_cache/html/top SVGs expression plot [multi]_92759d511bff77f76c7ce400fe52df34.RData
DESpace/vignettes/DESpace_cache/html/top SVGs expression plot [multi]_92759d511bff77f76c7ce400fe52df34.rdb
DESpace/vignettes/DESpace_cache/html/top SVGs expression plot [multi]_92759d511bff77f76c7ce400fe52df34.rdx
Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DESpace’ 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 ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [8s/8s] 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 ... [28s/28s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [1s/1s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [103s/151s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
DESpace_test 39.727 1.684 50.385
individual_test 24.313 0.636 62.336
FeaturePlot 22.269 0.486 24.842
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testhat.R’ [112s/117s]
[112s/117s] 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 ... [4s/5s] OK
* DONE
Status: 1 WARNING
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2946/DESpace_20230303163611/DESpace.Rcheck/00check.log’
for details.
===============================
BiocCheck('DESpace_0.99.0.tar.gz')
===============================
─ BiocCheckVersion: 1.35.12
─ BiocVersion: 3.17
─ Package: DESpace
─ PackageVersion: 0.99.0
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp4AZ4nH/file1fe0467da5d9/DESpace
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp4AZ4nH/file1fe01087fa8b
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2946/DESpace_20230303163611/DESpace.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...
* NOTE: Update R version dependency from 4.2.0 to 4.3.0.
* Checking package size...
* ERROR: Package tarball exceeds the Bioconductor size requirement.
* Checking individual file sizes...
* WARNING: The following files are over 5MB in size:
'vignettes/DESpace_cache/html/DESpace_14020df42a75f304ef9f2bf9bfae84f4.rdb
vignettes/DESpace_cache/html/load-example-data_fc37f89acfb45b875a69d2d28c7834e2.rdb
vignettes/DESpace_cache/html/QC
spots_27c6e94363b78704df31febb5891e5ef.rdb
vignettes/DESpace_cache/html/top SVGs expression plot
[multi]_92759d511bff77f76c7ce400fe52df34.rdb
vignettes/DESpace_cache/html/unnamed-chunk-11_b03235404c37479fd4bdc94cb7fab59a.rdb
vignettes/DESpace_cache/html/view LIBD layers
[multi]_979a23a988921dc7d56e6d9248cb9ce3.rdb'
* 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...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* 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 DESpace...
* Checking coding practice...
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 5 functions greater than 50 lines.
* Checking man page documentation...
* 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; 366 lines (13%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 50 lines
(2%) 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 ──
1 ERRORS | 1 WARNINGS | 7 NOTES
See the DESpace.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir DESpace_0.99.0.tar.gz'
>>>>>>>
* installing *source* package ‘DESpace’ ...
** 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 (DESpace)
===============================
R CMD BUILD
===============================
* checking for file ‘DESpace/DESCRIPTION’ ... OK
* preparing ‘DESpace’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘DESpace.Rmd’ using rmarkdown
Error running filter pandoc-citeproc:
Could not find executable pandoc-citeproc
Error: processing vignette 'DESpace.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed re-building ‘DESpace.Rmd’
SUMMARY: processing the following file failed:
‘DESpace.Rmd’
Error: Vignette re-building failed.
Execution halted