Question

Tibble error when installing bioconductor "airways"

0

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brest • 0

@brest-23222

Last seen 4.7 years ago

> BiocManager::install("airway")
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.3 (2020-02-29)
Installing package(s) 'airway'
installing the source package ‘airway’

essai de l'URL 'https://bioconductor.org/packages/3.10/data/experiment/src/contrib/airway_1.6.0.tar.gz'
Content type 'application/x-gzip' length 24226867 bytes (23.1 MB)
downloaded 23.1 MB

Warning: package incorrect 'C:\Users\xxxxx'
Warning: package incorrect 'xxxxxx\AppData\Local\Temp\RtmpGQ1B7u/downloaded_packages/airway_1.6.0.tar.gz'
Erreur : ERREUR : aucun package spécifié

The downloaded source packages are in
    ‘C:\Users\xxxxxxx\AppData\Local\Temp\RtmpGQ1B7u\downloaded_packages’
Old packages: 'tibble'
Update all/some/none? [a/s/n]: 
a

  There is a binary version available but the source version is later:
       binary source needs_compilation
tibble  2.1.3  3.0.0              TRUE

  Binaries will be installed
essai de l'URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/tibble_2.1.3.zip'
Content type 'application/zip' length 337382 bytes (329 KB)
downloaded 329 KB

package ‘tibble’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\XXXX\AppData\Local\Temp\RtmpGQ1B7u\downloaded_packages
Warning message:
In install.packages(...) :
  installation of package ‘airway’ had non-zero exit status

airway • 1.3k views

ADD COMMENT • link 4.7 years ago brest • 0

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> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252    LC_MONETARY=French_France.1252 LC_NUMERIC=C                  
[5] LC_TIME=French_France.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] IRanges_2.20.2      S4Vectors_0.24.3    BiocGenerics_0.32.0

loaded via a namespace (and not attached):
 [1] BiocManager_1.30.10 colorspace_1.4-1    scales_1.1.0        compiler_3.6.3      R6_2.4.1            tools_3.6.3        
 [7] RCurl_1.98-1.1      lifecycle_0.2.0     bitops_1.0-6        munsell_0.5.0       rlang_0.4.5

ADD REPLY • link updated 4.7 years ago by Martin Morgan 25k • written 4.7 years ago by brest • 0

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Michael Love 43k

@mikelove

Last seen 1 day ago

United States

Find the first package installation which had an error, and re-try installation of that package specifically.

ADD COMMENT • link 4.7 years ago Michael Love 43k

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done many times tibble comes from ggplot2 impossible to update

> BiocManager::install("airways")
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.3 (2020-02-29)
Installing package(s) 'airways'
Old packages: 'tibble'
Update all/some/none? [a/s/n]: 
a

  There is a binary version available but the source version is later:
       binary source needs_compilation
tibble  2.1.3  3.0.0              TRUE

  Binaries will be installed
essai de l'URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/tibble_2.1.3.zip'
Content type 'application/zip' length 337382 bytes (329 KB)
downloaded 329 KB

package ‘tibble’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\xxxxxx\AppData\Local\Temp\RtmpKyvpXI\downloaded_packages
Warning message:
package ‘airways’ is not available (for R version 3.6.3)

ADD REPLY • link updated 4.7 years ago by Martin Morgan 25k • written 4.7 years ago by brest • 0

2

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It ain't lying! airways is not available because...

> BiocManager::available("airw")
[1] "airway"              "pairwise"            "pairwiseCI"
[4] "pairwiseComparisons" "PairwiseD"           "RPPairwiseDesign"

it's singular airway.

ADD REPLY • link 4.7 years ago Martin Morgan 25k

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Try not updating tibble?

Also, try just using binary, not source version. <-- this has tripped up many users in the past. You don't need to install the later source version, you can often just use binary.

ADD REPLY • link 4.7 years ago Michael Love 43k

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brest • 0

@brest-23222

Last seen 4.7 years ago

Ok thank you very much. As you suggested, I created a session without space: it helps but not for the tibble problem By creating a session, I managed to install all package I needed from biocManager. But for this I should not install ggplot2 (that install tibble) before. If ggplot2 is intalled before, It is impossible to install anything from biocManager. Best regards

ADD COMMENT • link 4.7 years ago brest • 0

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It's usually better to show (simple) code illustrating the problem; I can't really tell whether you've had success or not, or what the problem might be.

ADD REPLY • link 4.7 years ago Martin Morgan 25k

score 3 · Accepted Answer · 2020-03-31

Note this part of the original installation attempt

Warning: package incorrect 'C:\Users\xxxxx'
Warning: package incorrect 'xxxxxx\AppData\Local\Temp\RtmpGQ1B7u/downloaded_packages/airway_1.6.0.tar.gz'

and how xxxxx is split in two. R is not reacting well to a (temporary) file path with spaces in it. You could try to set an environment variable TMPDIR pointing to a location without a space, although I'm not sure whether that is enough. I think you could also tackle this in two steps -- download the airway package

download.file("https://bioconductor.org/packages/3.10/data/experiment/src/contrib/airway_1.6.0.tar.gz", "airway_1.6.0.tar.gz")

and then install locally

install.packages("airway_1.6.0.tar.gz", repos = NULL)