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Are you a Microsoft Windows R user? Does your Windows username include a space? Like Firstname Lastname. Then you might occassionally run into issues installing packages due to spaces.
Solutions
You could either re-install Windows with a username that has no spaces such as Lastname1, but thatโs probably not an easy option. Or you can:
- Edit your
TMPandTEMPenvironment variables to a location with no spaces, likeC:\TEMPfollowing instructions like these ones. - Preferably install
Rat a location with no spaces, likeC:\R, instead of the defaultC:\Program Files2.
Backstory
A co-worker wanted to install the clusterprofiler Bioconductor package which depends on the DO.db Bioconductor package. This co-worker uses a Windows machine that has a username with a space. Letโs say it was me with Leo Collado to keep them anonymous. The DO.db is only available as a โSourceโ package with no Windows binary as you can see here.
This means that R has to:
- download a
tar.gzfile, - uncompress it,
- and then install it.
In particular, we are talking about DO.db_2.9.tar.gz in this case.
The installation instructions for DO.db are:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("DO.db")Uncompressing
Internally, BiocManager::install() ends up using utils::install.packages(). The first step, downloading, works well. Uncompressing a file in this scenario fails. Why?
> BiocManager::install('DO.db', lib = 'C:/R/R-3.6.0/library')Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)Installing package(s) 'BiocVersion', 'DO.db'## removed outputtrying URL 'https://bioconductor.org/packages/3.9/data/annotation/src/contrib/DO.db_2.9.tar.gz'Content type 'application/x-gzip' length 1769978 bytes (1.7 MB)downloaded 1.7 MBError in untar2(tarfile, files, list, exdir, restore_times) : incomplete block on fileThe downloaded source packages are in โC:\Users\Leo Collado\AppData\Local\Temp\RtmpqiBJ53\downloaded_packagesโIf you search on Google the error message youโll find links like this one which hint towards an incomplete download. But the download works. You can even download the file and try to run untar() manually and it will fail.
We were told to try installing R at a location with no spaces, so by this point, R was installed at C:\R\R-3.6.0\, hence the lib specification you see above, though itโs irrelevant for these errors.
Uncompressing the tar.gz file is done by utils::untar(). If you look at the code for utils::untar() youโll see:
## The function definition of utils::untarfunction (tarfile, files = NULL, list = FALSE, exdir = ".", compressed = NA, extras = NULL, verbose = FALSE, restore_times = TRUE, support_old_tars = Sys.getenv("R_SUPPORT_OLD_TARS", FALSE), tar = Sys.getenv("TAR")) ## Inside utils::untar()if (inherits(tarfile, "connection") || identical(tar, "internal")) { if (!missing(compressed)) warning("argument 'compressed' is ignored for the internal method") return(untar2(tarfile, files, list, exdir, restore_times))}## Further belowTAR <- tarif (!nzchar(TAR) && .Platform$OS.type == "windows" && nzchar(Sys.which("tar.exe"))) TAR <- "tar.exe"if (!nzchar(TAR) || TAR == "internal") return(untar2(tarfile, files, list, exdir))In this case, the first untar2() call is called. That is: return(untar2(tarfile, files, list, exdir, restore_times)). The error message incomplete block on file is not really informative in this case because untar2() is not happy when thereโs a space in the path to the file 3.
We can get around this untar2() issue by uncompressing the tar.gz file ourselves in a path that has no spaces. For example, if we download DO.db_2.9.tar.gz to C:\R we can uncompress the tar.gz file with:
utils::untar('C:/R/DO.db_2.9.tar.gz')Installation
Letโs proceed to installing the package.
> install.packages('C:/R/DO.db', repos = NULL, type = 'source', lib = 'C:/R/R-3.6.0/library')* installing *source* package 'DO.db' ...** using staged installation** R** inst** byte-compile and prepare package for lazy loadingARGUMENT 'Collado\AppData\Local\Temp\Rtmp8EQDjB\Rin2ef05088650f' __ignored__Error: object 'รฟรพ' not foundExecution haltedERROR: lazy loading failed for package 'DO.db'* removing 'C:/R/R-3.6.0/library/DO.db'Warning message:In install.packages("C:/R/DO.db", repos = NULL, type = "source", : installation of package โC:/R/DO.dbโ had non-zero exit status>Oh noes! It didnโt work 
What happened?
If you look closely, youโll see that it says ARGUMENT 'Collado\AppData\Local\Temp\Rtmp8EQDjB\Rin2ef05088650f' __ignored__. Wait! Collado is the Lastname portion of the username! So we have another space issue 4. That structure though looks very familiar, itโs from base::tempdir()!
> tempdir()[1] "C:\\Users\\Leo Collado\\AppData\\Local\\Temp\\RtmpqiBJ53"The help file for ?tempdir contained the clues to solving this issue.
By default, tmpdir will be the directory given by tempdir(). This will be a subdirectory of the per-session temporary directory found by the following rule when the R session is started. The environment variables TMPDIR, TMP and TEMP are checked in turn and the first found which points to a writable directory is used: if none succeeds โ/tmpโ is used. The path should not contain spaces. Note that setting any of these environment variables in the R session has no effect on tempdir(): the per-session temporary directory is created before the interpreter is started.
We can set the TMPDIR environment variable which will be used by the R session spawned inside the installation of DO.db andโฆ it works!
> Sys.setenv(TMPDIR = 'C:/R/tmp_leo')> Sys.getenv('TMPDIR')[1] "C:/R/tmp_leo">>> install.packages('C:/R/DO.db', repos = NULL, type = 'source', lib = 'C:/R/R-3.6.0/library')* installing *source* package 'DO.db' ...** using staged installation** R** inst** byte-compile and prepare package for lazy loading** help*** installing help indices converting help for package 'DO.db' finding HTML links ... done DOANCESTOR html DOBASE html DOCHILDREN html DOMAPCOUNTS html DOOBSOLETE html DOOFFSPRING html DOPARENTS html DOSYNONYM html DOTERM html DOTerms-class html DOTermsAnnDbBimap html DO_dbconn html ** building package indices** testing if installed package can be loaded from temporary location*** arch - i386*** arch - x64** testing if installed package can be loaded from final location*** arch - i386*** arch - x64** testing if installed package keeps a record of temporary installation path* DONE (DO.db)Making 'packages.html' ... doneclusterProfiler installation
Now we can continue and install clusterProfiler, right?
> BiocManager::install('clusterProfiler', lib = 'C:/R/R-3.6.0/library')Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)Installing package(s) 'clusterProfiler'also installing the dependencies โsysโ, โformatRโ, โaskpassโ, โfarverโ, โbackportsโ, โzeallotโ, โlambda.rโ, โfutile.optionsโ, โcurlโ, โmimeโ, โopensslโ, โhmsโ, โtriebeardโ, โtweenrโ, โpolyclipโ, โRcppEigenโ, โcolorspaceโ, โutf8โ, โvctrsโ, โfutile.loggerโ, โsnowโ, โdata.tableโ, โfastmatchโ, โstringrโ, โhttrโ, โjsonliteโ, โprogressโ, โurltoolsโ, โxml2โ, โgridGraphicsโ, โggforceโ, โggrepelโ, โviridisโ, โlabelingโ, โmunsellโ, โR6โ, โcliโ, โcrayonโ, โfansiโ, โpillarโ, โBiocParallelโ, โfgseaโ, โreshape2โ, โcowplotโ, โeuropepmcโ, โggplotifyโ, โggraphโ, โggridgesโ, โgridExtraโ, โigraphโ, โpurrrโ, โRColorBrewerโ, โUpSetRโ, โgtableโ, โlazyevalโ, โrlangโ, โscalesโ, โtibbleโ, โviridisLiteโ, โwithrโ, โdplyrโ, โglueโ, โstringiโ, โtidyselectโ, โDOSEโ, โenrichplotโ, โggplot2โ, โGO.dbโ, โGOSemSimโ, โplyrโ, โqvalueโ, โrvcheckโ, โtidyrโ## Delete more outputThe downloaded binary packages are in C:\Users\Leo Collado\AppData\Local\Temp\RtmpqiBJ53\downloaded_packagesinstalling the source packages โpillarโ, โGO.dbโtrying URL 'https://cloud.r-project.org/src/contrib/pillar_1.4.1.tar.gz'Content type 'application/x-gzip' length 228572 bytes (223 KB)downloaded 223 KBtrying URL 'https://bioconductor.org/packages/3.9/data/annotation/src/contrib/GO.db_3.8.2.tar.gz'Content type 'application/x-gzip' length 31820866 bytes (30.3 MB)downloaded 30.3 MBError in untar2(tarfile, files, list, exdir, restore_times) : incomplete block on fileError in untar2(tarfile, files, list, exdir, restore_times) : incomplete block on fileThe downloaded source packages are in โC:\Users\Leo Collado\AppData\Local\Temp\RtmpqiBJ53\downloaded_packagesโThe issue is again that utils:::untar2() and thus utils::untar() does not like spaces in the paths. If we look at where the packages were downloaded more closely, we can see a space there at C:\Users\Leo Collado\AppData\Local\Temp\RtmpqiBJ53\downloaded_packages. If you check the help file for utils::install.packages() youโll see that destdir controls this:
destdir
directory where downloaded packages are stored. If it is NULL (the default) a subdirectory downloaded_packages of the session temporary directory will be used (and the files will be deleted at the end of the session).
If we dig into utils::install.packages() we can see how this comes to play.
## Part of utils::install.packages()if (is.null(destdir) && nonlocalrepos) { tmpd <- file.path(tempdir(), "downloaded_packages") if (!file.exists(tmpd) && !dir.create(tmpd)) stop(gettextf("unable to create temporary directory %s", sQuote(tmpd)), domain = NA)}Setting the environment variable TMPDIR doesnโt work here as the instructions for tempdir() specify 5 although I now see that you can edit the .Renviron file as instructed here.
In any case, if we specify a destdir without spaces we overide the need to control tempdir(), enable utils::untar() to work and we can finally install clusterProfiler
.
> BiocManager::install('clusterProfiler', lib = 'C:/R/R-3.6.0/library', destdir = 'C:/R/dest_leo')Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)Installing package(s) 'clusterProfiler'also installing the dependency โGO.dbโtrying URL 'https://bioconductor.org/packages/3.9/bioc/bin/windows/contrib/3.6/clusterProfiler_3.12.0.zip'Content type 'application/zip' length 623524 bytes (608 KB)downloaded 608 KBpackage โclusterProfilerโ successfully unpacked and MD5 sums checkedinstalling the source package โGO.dbโtrying URL 'https://bioconductor.org/packages/3.9/data/annotation/src/contrib/GO.db_3.8.2.tar.gz'Content type 'application/x-gzip' length 31820866 bytes (30.3 MB)downloaded 30.3 MB* installing *source* package 'GO.db' ...** using staged installation** R** inst** byte-compile and prepare package for lazy loading** help*** installing help indices converting help for package 'GO.db' finding HTML links ... done GOBASE html GOBPANCESTOR html GOBPCHILDREN html GOBPOFFSPRING html GOBPPARENTS html GOCCANCESTOR html GOCCCHILDREN html GOCCOFFSPRING html GOCCPARENTS html GOMAPCOUNTS html GOMFANCESTOR html GOMFCHILDREN html GOMFOFFSPRING html GOMFPARENTS html GOOBSOLETE html GOSYNONYM html GOTERM html GO_dbconn html ** building package indices** testing if installed package can be loaded from temporary location*** arch - i386*** arch - x64** testing if installed package can be loaded from final location*** arch - i386*** arch - x64** testing if installed package keeps a record of temporary installation path* DONE (GO.db)Making 'packages.html' ... doneClosing
All of the above seemed like too much. In addition, it seemed like BiocManager::install('hypeR', destdir = 'C:/R/dest_leo') was not working 6. I likely missed something here earlier today. So controlling utils::tempdir() seemed like the easiest solution such that the defaults of where a package gets downloaded, uncompressed, etc all worked. And the simplest solution we thought of was to create the C:\TEMP directory and update the Windows environment variables TMP and TEMP to point to that location. Then, the rest of the commands worked without having to specify lib or destdir or manually run utils::untar().
As a whole, remember to look for spaces in the error messages! This is specially relevant when you are having issues as a Microsoft Windows R user.
If you have other solutions for Microsoft Windows R users with usernames that have at least one space, please let us know in the comments! Thank you! 
Acknowledgements
This blog post was made possible thanks to:
References
[1] C. Boettiger. knitcitations: Citations for โKnitrโ Markdown Files. R package version 1.0.8. 2017. URL: https://CRAN.R-project.org/package=knitcitations.
[2] G. Csรกrdi, R. core, H. Wickham, W. Chang, et al. sessioninfo: R Session Information. R package version 1.1.1. 2018. URL: https://CRAN.R-project.org/package=sessioninfo.
[3] A. Oleล, M. Morgan, and W. Huber. BiocStyle: Standard styles for vignettes and other Bioconductor documents. R package version 2.12.0. 2019. URL: https://github.com/Bioconductor/BiocStyle.
[4] Y. Xie, A. P. Hill, and A. Thomas. blogdown: Creating Websites with R Markdown. ISBN 978-0815363729. Boca Raton, Florida: Chapman and Hall/CRC, 2017. URL: https://github.com/rstudio/blogdown.
Reproducibility
## โ Session info โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ## setting value ## version R version 3.6.1 (2019-07-05)## os macOS Mojave 10.14.6 ## system x86_64, darwin15.6.0 ## ui X11 ## language (EN) ## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz America/New_York ## date 2019-09-18 ## ## โ Packages โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ## package * version date lib source ## assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0) ## bibtex 0.4.2 2017-06-30 [1] CRAN (R 3.6.0) ## BiocManager 1.30.4 2018-11-13 [1] CRAN (R 3.6.0) ## BiocStyle * 2.12.0 2019-05-02 [1] Bioconductor ## blogdown 0.15 2019-08-21 [1] CRAN (R 3.6.1) ## bookdown 0.13 2019-08-21 [1] CRAN (R 3.6.0) ## cli 1.1.0 2019-03-19 [1] CRAN (R 3.6.0) ## colorout * 1.2-1 2019-05-07 [1] Github (jalvesaq/colorout@7ea9440)## crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0) ## digest 0.6.20 2019-07-04 [1] CRAN (R 3.6.0) ## evaluate 0.14 2019-05-28 [1] CRAN (R 3.6.0) ## htmltools 0.3.6 2017-04-28 [1] CRAN (R 3.6.0) ## httr 1.4.1 2019-08-05 [1] CRAN (R 3.6.0) ## jsonlite 1.6 2018-12-07 [1] CRAN (R 3.6.0) ## knitcitations * 1.0.8 2017-07-04 [1] CRAN (R 3.6.0) ## knitr 1.24 2019-08-08 [1] CRAN (R 3.6.0) ## lubridate 1.7.4 2018-04-11 [1] CRAN (R 3.6.0) ## magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.0) ## plyr 1.8.4 2016-06-08 [1] CRAN (R 3.6.0) ## R6 2.4.0 2019-02-14 [1] CRAN (R 3.6.0) ## Rcpp 1.0.2 2019-07-25 [1] CRAN (R 3.6.0) ## RefManageR 1.2.12 2019-04-03 [1] CRAN (R 3.6.0) ## rmarkdown 1.15 2019-08-21 [1] CRAN (R 3.6.1) ## sessioninfo * 1.1.1 2018-11-05 [1] CRAN (R 3.6.0) ## stringi 1.4.3 2019-03-12 [1] CRAN (R 3.6.0) ## stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.0) ## withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0) ## xfun 0.9 2019-08-21 [1] CRAN (R 3.6.0) ## xml2 1.2.2 2019-08-09 [1] CRAN (R 3.6.0) ## yaml 2.2.0 2018-07-25 [1] CRAN (R 3.6.0) ## ## [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/libraryThis is the case in the Bioconductor Windows build machine where the username is
biocbuildas you can see here.![โฉ]()
In the Bioconductor Windows build machines there are again no spaces in the path to the R installation and the library where packages are installed.
![โฉ]()
Hopefully in the future Google will lead you to this blog post and you might avoid the rabbit hole I went through!
![โฉ]()
By the way, at this point I thought that the error was related to
Error: object 'รฟรพ' not foundand maybe some encoding issues since the DO.db package has Chinese characters.![โฉ]()
Didnโt stop me from trying hehe. I tried using
usethis::edit_r_profile()and addingSys.setenv(TMPDIR = 'C:/R/tmp_leo')but that didnโt work.![โฉ]()
I would need to test this more before reporting it properly to Bioconductor.
![โฉ]()
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