Install Problem

[aviezerl]

Original report by Yue Wu (Bitbucket: 5caa79174353071e5657a01a, ).

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Hi there~

Hope all is good! I am creating this issue because I come across such problem when trying to install the Metacell package in R.

install.packages("BiocManager")
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.5/BiocManager_1.30.4.tgz'
Content type 'application/x-gzip' length 287459 bytes (280 KB)
==================================================
downloaded 280 KB

The downloaded binary packages are in
/var/folders/0_/sfnkh6s95xsb48vt4w2ytsbr1b5tp_/T//RtmpuhOyVK/downloaded_packages

BiocManager::install('metacell', site_repository = 'tanaylab.bitbucket.io/repo', update = FALSE)
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.3 (2019-03-11)
Installing package(s) 'metacell'
also installing the dependencies ‘data.table’, ‘tgutil’

Warning: unable to access index for repository tanaylab.bitbucket.io/repo/bin/macosx/el-capitan/contrib/3.5:
cannot open URL 'tanaylab.bitbucket.io/repo/bin/macosx/el-capitan/contrib/3.5/PACKAGES'

There is a binary version available but the source version is later:
binary source needs_compilation
data.table 1.12.0 1.12.2 TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes
installing the source packages ‘data.table’, ‘tgutil’, ‘metacell’

trying URL 'https://cran.rstudio.com/src/contrib/data.table_1.12.2.tar.gz'
Content type 'application/x-gzip' length 3343698 bytes (3.2 MB)

downloaded 3.2 MB

trying URL 'tanaylab.bitbucket.io/repo/src/contrib/tgutil_0.1.2.tar.gz'
Content type 'application/x-tar' length 38788 bytes (37 KB)

downloaded 37 KB

trying URL 'tanaylab.bitbucket.io/repo/src/contrib/metacell_0.3.39.tar.gz'
Content type 'application/x-tar' length 5318621 bytes (5.1 MB)

downloaded 5.1 MB

• installing source package ‘data.table’ ...
  ** package ‘data.table’ successfully unpacked and MD5 sums checked
  ** libs
  clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c assign.c -o assign.o
  clang: error: unsupported option '-fopenmp'
  make: *** [assign.o] Error 1
  ERROR: compilation failed for package ‘data.table’
• removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/data.table’
  ERROR: dependency ‘data.table’ is not available for package ‘tgutil’
• removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/tgutil’
  ERROR: dependencies ‘data.table’, ‘tgutil’ are not available for package ‘metacell’
• removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/metacell’

The downloaded source packages are in
‘/private/var/folders/0_/sfnkh6s95xsb48vt4w2ytsbr1b5tp_/T/RtmpuhOyVK/downloaded_packages’

library(metacell)
Error in library(metacell) : there is no package called ‘metacell’

Could you please kindly help with with the problem?

Thank you so much!

[aviezerl]

Original comment by Aviezer Lifshitz (Bitbucket: 557058:bf6ad907-8661-42ac-8d8b-37c2b536b4b1, GitHub: aviezerl).

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Hi Yue,

It seems like a problem of data.table:

Rdatatable/data.table#2875

Please install data.table separately from binary by running:

install.packages("data.table")

And then retry installing metacell.

Best,

Aviezer

[aviezerl]

Original comment by Yue Wu (Bitbucket: 5caa79174353071e5657a01a, ).

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Hi Aviezer,

Sorry for the delayed reply, and thank you so much for the kind assistance. The problem was solved.

Best regards,
Yue