search

Bioconductor / basilisk

Clone of the Bioconductor repository for the basilisk package.
https://bioconductor.org/packages/devel/bioc/html/basilisk.html
GNU General Public License v3.0
26 stars 14 forks source link

Installation of basilisk under R 4.4.1 fails #43

Open joachimt1 opened 1 week ago

joachimt1 commented 1 week ago

I've been trying to install the R package for 'basilisk' under deployment of R on a Mac Powerbook (macOS 14.4.1 Sonoma) but am getting an error :

[1] "R version 4.4.1 (2024-06-14)"

BiocManager::install("basilisk") Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.1 (2024-06-14) Installing package(s) 'basilisk' installing the source package ‘basilisk’

trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/basilisk_1.16.0.tar.gz' Content type 'application/x-gzip' length 264252 bytes (258 KB)

downloaded 258 KB

I get the same error message if Iattempt to directly install from the tarball , e.g. through :

  install.packages("../packages-as-tarballs/basilisk_1.16.0.tar.gz", repos=NULL);

Is there an easy fix to this problem?

Many Thanks, Joachim

vjcitn commented 1 week ago

I don't have access to a mac platform right now. What you report looks like a systemic problem with package installation. Can you install, e.g., Biobase?

joachimt1 commented 1 week ago

Thanks for your prompt answer! I haven't tried Biobase explicitly, but I can install a whole bunch of other BioConductor packages, including :

    apBIO = c("ctc",                                                  "DAVIDQuery",               "limma",                                               "affy",                                               "geneplotter",               "impute",                                               "sva",                                                 "GEOquery",               "ComplexHeatmap",               "edgeR",               "DESeq2",               "DESeq",               "biomaRt",               "monocle",              "org.Hs.eg.db",              "org.Mm.eg.db",                    "outliers",              "pbmcapply",              "GSEABase",               "GSVA",               "doFuture",              "singscore",              "doParallel",              "SingleR",              "rhdf5",              "scDblFinder",              "scds",              "hdf5r"); All of these install seamlessly using BiocManager() .  .  . Best regards,Joachim

Joachim (Kim) Theilhaber, PhDcomputational biology/bioinformatics Epileptosmobile +1 617 460 2925 Cambridge, Massachusetts @.***://www.linkedin.com/in/joachim-theilhaber-69849b3/

On Monday, July 1, 2024 at 10:58:56 AM EDT, Vince Carey ***@***.***> wrote:

I don't have access to a mac platform right now. What you report looks like a systemic problem with package installation. Can you install, e.g., Biobase?

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

LTLA commented 6 days ago

If I had to guess, I'd say that your R installation is somehow misconfigured, i.e., Rscript can't find the R binary. Looking up the error suggests that this occurs if R is moved after installation, see here.

I don't have access to my Mac right now, but last I remember, basilisk was working fine on my homebrew setup.

vjcitn commented 6 days ago

Here's what happens on my mac:

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

1/12 packages newly attached/loaded, see sessionInfo() for details.
> BiocManager::install("basilisk", force=TRUE)
Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.1 (2024-06-14)
Installing package(s) 'basilisk'
trying URL 'https://bioconductor.org/packages/3.19/bioc/bin/macosx/big-sur-arm64/contrib/4.4/basilisk_1.16.0.tgz'
Content type 'application/x-gzip' length 313468 bytes (306 KB)
==================================================
downloaded 306 KB

Notice that this is a binary package with .tgz suffix. Most mac users will get/use this. Why are you installing from source on a mac? When I explicitly ask for installation of basilisk from source, it works.

> sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.2.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

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

other attached packages:
[1] rmarkdown_2.27

loaded via a namespace (and not attached):
 [1] BiocManager_1.30.23 compiler_4.4.1      startup_0.21.0     
 [4] fastmap_1.2.0       cli_3.6.3           tools_4.4.1        
 [7] htmltools_0.5.8.1   knitr_1.47          xfun_0.45          
[10] digest_0.6.36       rlang_1.1.4         evaluate_0.24.0
joachimt1 commented 6 days ago

HiThanks much for your latest message. Below is the equivalent session on my mac computer. As you can see, the BiocManager call automatically tries to compile from source, invoking the .tar.gz file instead of the .tgz file as in your case but fails.  ---------------------------------------------------------------------------------------------------------------------------------------R version 4.4.1 (2024-06-14) -- "Race for Your Life"Copyright (C) 2024 The R Foundation for Statistical ComputingPlatform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY.You are welcome to redistribute it under certain conditions.Type 'license()' or 'licence()' for distribution details.   Natural language support but running in an English locale R is a collaborative project with many contributors.Type 'contributors()' for more information and'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or'help.start()' for an HTML browser interface to help.Type 'q()' to quit R.

setwd('/Users/joachimt1/develop/R-Programs')options(chmhelp=FALSE)> > options(htmlhelp=TRUE)> library(BiocManager)Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.1 (2024-06-14)>        BiocManager::install("basilisk", force = TRUE);Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.1 (2024-06-14)Installing package(s) 'basilisk'installing the source package ‘basilisk’ trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/basilisk_1.16.0.tar.gz'Content type 'application/x-gzip' length 264252 bytes (258 KB)==================================================downloaded 258 KB

  • installing source package ‘basilisk’ ...* using non-staged installation via StagedInstall fieldRscript execution error: No such file or directoryERROR: configuration failed for package ‘basilisk’ removing ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/basilisk’ The downloaded source packages are in ‘/private/var/folders/b0/1k4b4_5j3s99sxs5g3pmxrvh0000gn/T/RtmpDGSwBJ/downloaded_packages’Warning message:In install.packages(...) :  installation of package ‘basilisk’ had non-zero exit status>  ------------------------------------------------------------------------------------------------------------------- Trying to directly load from a binary does not work however : ------------------------------------------------------------------------------------------------------------------- > BiocManager::install("basilisk", force = TRUE, type = "binary")Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.1 (2024-06-14)Installing package(s) 'basilisk'    package ‘basilisk’ is available as a source package but not as a binary Warning message:package ‘basilisk’ is not available as a binary package for Bioconductor version '3.19' A version of this package for your version of R might be available elsewhere,see the ideas athttps://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages > ----------------------------------------------------------------------------------------------------------------

Are the R-relevant environment variables OK and can they matter ?

Sys.getenv() R_ARCH                  R_BROWSER               /usr/bin/openR_BZIPCMD               /usr/bin/bzip2R_DOC_DIR               /Library/Frameworks/R.framework/Resources/docR_GZIPCMD               /usr/bin/gzipR_HOME                  /Library/Frameworks/R.framework/ResourcesR_INCLUDE_DIR           /Library/Frameworks/R.framework/Resources/includeR_LIBS_SITE             /Library/Frameworks/R.framework/Resources/site-libraryR_LIBS_USER             /Users/joachimt1/Library/R/x86_64/4.4/libraryR_PAPERSIZE             a4R_PDFVIEWER             /usr/bin/openR_PLATFORM              x86_64-apple-darwin20R_PRINTCMD              lprR_QPDF                  /Library/Frameworks/R.framework/Resources/bin/qpdfR_RD4PDF                times,inconsolata,hyperR_SESSION_TMPDIR        /var/folders/b0/1k4b4_5j3s99sxs5g3pmxrvh0000gn/T//RtmpDGSwBJR_SHARE_DIR             /Library/Frameworks/R.framework/Resources/shareR_STRIP_SHARED_LIB      strip -xR_STRIP_STATIC_LIB      strip -SR_TEXI2DVICMD           /opt/R/x86_64/bin/texi2dviR_UNZIPCMD              /usr/bin/unzipR_ZIPCMD                /usr/bin/zip RHOME                   /Library/Frameworks/R.framework/Resources/bin----------------------------------------------------------------------------------------------------------------

Thanks again,Joachim On Tue, Jul 2, 2024 at 4:56, Vince @.***> wrote:

Here's what happens on my mac: R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.

1/12 packages newly attached/loaded, see sessionInfo() for details.

BiocManager::install("basilisk", force=TRUE) Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.1 (2024-06-14) Installing package(s) 'basilisk' trying URL 'https://bioconductor.org/packages/3.19/bioc/bin/macosx/big-sur-arm64/contrib/4.4/basilisk_1.16.0.tgz' Content type 'application/x-gzip' length 313468 bytes (306 KB)

downloaded 306 KB

Notice that this is a binary package with .tgz suffix. Most mac users will get/use this. Why are you installing from source on a mac? When I explicitly ask for installation of basilisk from source, it works.

sessionInfo() R version 4.4.1 (2024-06-14) Platform: aarch64-apple-darwin20 Running under: macOS Sonoma 14.2.1

Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York tzcode source: internal

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

other attached packages: [1] rmarkdown_2.27

loaded via a namespace (and not attached): [1] BiocManager_1.30.23 compiler_4.4.1 startup_0.21.0
[4] fastmap_1.2.0 cli_3.6.3 tools_4.4.1
[7] htmltools_0.5.8.1 knitr_1.47 xfun_0.45
[10] digest_0.6.36 rlang_1.1.4 evaluate_0.24.0

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

joachimt1 commented 6 days ago

And also I note that R does seem to know where Rscript is : -------------------------------------------------------------------------------Sys.which("Rscript")                                                Rscript "/Library/Frameworks/R.framework/Resources/bin/Rscript" ------------------------------------------------------------------------------ which is the valid location. --Joachim

Joachim (Kim) Theilhaber, PhDcomputational biology/bioinformatics Epileptosmobile +1 617 460 2925 Cambridge, Massachusetts @.***://www.linkedin.com/in/joachim-theilhaber-69849b3/

On Tuesday, July 2, 2024 at 04:56:26 AM EDT, Vince Carey ***@***.***> wrote:

Here's what happens on my mac: R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.

1/12 packages newly attached/loaded, see sessionInfo() for details.

BiocManager::install("basilisk", force=TRUE) Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.1 (2024-06-14) Installing package(s) 'basilisk' trying URL 'https://bioconductor.org/packages/3.19/bioc/bin/macosx/big-sur-arm64/contrib/4.4/basilisk_1.16.0.tgz' Content type 'application/x-gzip' length 313468 bytes (306 KB)

downloaded 306 KB

Notice that this is a binary package with .tgz suffix. Most mac users will get/use this. Why are you installing from source on a mac? When I explicitly ask for installation of basilisk from source, it works.

sessionInfo() R version 4.4.1 (2024-06-14) Platform: aarch64-apple-darwin20 Running under: macOS Sonoma 14.2.1

Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York tzcode source: internal

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

other attached packages: [1] rmarkdown_2.27

loaded via a namespace (and not attached): [1] BiocManager_1.30.23 compiler_4.4.1 startup_0.21.0
[4] fastmap_1.2.0 cli_3.6.3 tools_4.4.1
[7] htmltools_0.5.8.1 knitr_1.47 xfun_0.45
[10] digest_0.6.36 rlang_1.1.4 evaluate_0.24.0

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

vjcitn commented 6 days ago

why not try to get the .tgz from https://bioconductor.org/packages/release/bioc/html/basilisk.html scroll down

joachimt1 commented 6 days ago

Unfortunately it looks like I would need the binary compiled for the x86_64 platform (my mac being a  venerable 4 years old).

or at least I imagine that is the problem.Am I invoking he installation function correctly below? -----------------------------------------------------------------------------------------------------       install.packages("../packages-as-tarballs/basilisk_1.16.0.tgz", repos=NULL);tar: Error opening archive: Failed to open '../packages-as-tarballs/basilisk_1.16.0.tgz'Error: file ‘../packages-as-tarballs/basilisk_1.16.0.tgz’ is not a macOS binary packageIn addition: Warning message:'tar' returned non-zero exit code 1 ----------------------------------------------------------------------------------------------------- Joachim (Kim) Theilhaber, PhDcomputational biology/bioinformatics Epileptosmobile +1 617 460 2925 Cambridge, Massachusetts @.***://www.linkedin.com/in/joachim-theilhaber-69849b3/

   

On Tuesday, July 2, 2024 at 10:03:36 AM EDT, Vince Carey ***@***.***> wrote:

why not try to get the .tgz from https://bioconductor.org/packages/release/bioc/html/basilisk.html scroll down

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

LTLA commented 6 days ago

And also I note that R does seem to know where Rscript is :

That's not the problem. The error message indicates that Rscript doesn't know where R is.

Anyway, installation works fine on my Mac:

> BiocManager::install("basilisk", force=TRUE)
Bioconductor version 3.20 (BiocManager 1.30.23), R 4.4.1 Patched (2024-06-20
  r86796)
Installing package(s) 'basilisk'
trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/basilisk_1.17.0.tar.gz'
Content type 'application/x-gzip' length 267961 bytes (261 KB)
==================================================
downloaded 261 KB

* installing *source* package ‘basilisk’ ...
** using non-staged installation via StagedInstall field
** 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
* DONE (basilisk)

The downloaded source packages are in
    ‘/private/var/folders/ls/f3g2mn9x77j5ngg5f4hg0qy40000gn/T/RtmpQsSQHq/downloaded_packages’

I'm using BioC-devel on this machine but there shouldn't be any difference with BioC-release.

joachimt1 commented 6 hours ago

Hi again, I installed the latest version of R on my mac, successfully re-installed > 100 packages, BUT installation of  basilisk keep failing with the same message. Might this be because the path variable that is not correctly set? R.Version()[["version.string"]][1] "R version 4.4.1 (2024-06-14)"> BiocManager::install("basilisk", force=TRUE)Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.1 (2024-06-14)Installing package(s) 'basilisk'installing the source package ‘basilisk’ trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/basilisk_1.16.0.tar.gz'Content type 'application/x-gzip' length 264252 bytes (258 KB)==================================================downloaded 258 KB

Joachim (Kim) Theilhaber, PhDcomputational biology/bioinformatics Epileptosmobile +1 617 460 2925 Cambridge, Massachusetts @.***://www.linkedin.com/in/joachim-theilhaber-69849b3/

[joachimt1 /Library/Frameworks/R.framework/Resources/bin] (7) > pwd/Library/Frameworks/R.framework/Resources/bin[joachimt1 /Library/Frameworks/R.framework/Resources/bin] (8) > ltotal 11816-rwxrwxr-x  1 root  admin     1838 Jun 15 13:39 BATCH-rwxrwxr-x  1 root  admin     2168 Jun 15 13:39 COMPILE-rwxrwxr-x  1 root  admin      825 Jun 15 13:39 INSTALL-rwxrwxr-x  1 root  admin     1324 Jun 15 13:39 LINK-rwxrwxr-x  1 root  admin     9255 Jun 15 13:39 R-rwxrwxr-x  1 root  admin      160 Jun 15 13:39 REMOVE-rwxrwxr-x  1 root  admin     1426 Jun 15 13:39 Rcmd-rwxrwxr-x  1 root  admin      318 Jun 15 13:39 Rd2pdf-rwxrwxr-x  1 root  admin      361 Jun 15 13:39 Rdconv-rwxrwxr-x  1 root  admin      260 Jun 15 13:39 Rdiff-rwxrwxr-x  1 root  admin      312 Jun 15 13:39 Rprof-rwxrwxr-x  1 root  admin    70944 Jun 15 13:43 Rscript-rwxrwxr-x  1 root  admin      157 Jun 15 13:39 SHLIB-rwxrwxr-x  1 root  admin      320 Jun 15 13:39 Stangle-rwxrwxr-x  1 root  admin      318 Jun 15 13:39 Sweave-rwxrwxr-x  1 root  admin      352 Jun 15 13:39 build-rwxrwxr-x  1 root  admin      319 Jun 15 13:39 check-rwxrwxr-x  1 root  admin    12483 Jun 15 13:39 configdrwxrwxr-x  3 root  admin       96 Jun 15 13:43 exec/-rwxrwxr-x  1 root  admin  3087968 Jun 15 13:43 fc-cache-rwxrwxr-x  1 root  admin    14552 Jun 15 13:39 javareconf-rwxrwxr-x  1 root  admin   350599 Jun 15 13:39 libtool-rwxrwxr-x  1 root  admin     3494 Jun 15 13:39 mkinstalldirs-rwxrwxr-x  1 root  admin      481 Jun 15 13:39 pager-rwxrwxr-x  1 root  admin  2412336 Jun 15 13:43 qpdf-rwxrwxr-x  1 root  admin     4700 Jun 15 13:39 rtags*[joachimt1 /Library/Frameworks/R.framework/Resources/bin] (9) >  On Tuesday, July 2, 2024 at 01:49:32 PM EDT, Aaron Lun @.***> wrote:

And also I note that R does seem to know where Rscript is :

That's not the problem. The error message indicates that Rscript doesn't know where R is.

Anyway, installation works fine on my Mac:

BiocManager::install("basilisk", force=TRUE) Bioconductor version 3.20 (BiocManager 1.30.23), R 4.4.1 Patched (2024-06-20 r86796) Installing package(s) 'basilisk' trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/basilisk_1.17.0.tar.gz' Content type 'application/x-gzip' length 267961 bytes (261 KB)

downloaded 261 KB

The downloaded source packages are in ‘/private/var/folders/ls/f3g2mn9x77j5ngg5f4hg0qy40000gn/T/RtmpQsSQHq/downloaded_packages’

I'm using BioC-devel on this machine but there shouldn't be any difference with BioC-release.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

LTLA commented 5 hours ago
  1. I don't know what path variable you're referring to.
  2. The problem is still with your Rscript. Check if you can run anything at all with /Library/Frameworks/R.framework/Resources/bin/Rscript.
  3. Format your code properly with backticks, it's a pain to read your posts.