Bioconductor installation problems
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Entering edit mode
jose ▴ 10
@2f84d272
Last seen 2.6 years ago
United States

Dear Friends,

I have been having considerable difficulty doing various package related bioconductor actions. Here is my system specifications:

======================================================================= macOS Monterey Version: 12.3 (21E230)

MacBook Pro (Retina, 13-inch, Early 2015) Memory: 16 GB 1867 MHz DDR3

RStudio 2021.09.0 Build 351

R version 4.1.2 (2021-11-01) -- "Bird Hippie" Copyright (C) 2021 The R Foundation for Statistical Computing

Platform: x86_64-apple-darwin17.0 (64-bit)

While the problem I have seems to be related to similar ones reported here, I'm not sure what the problem is. Very similar error messages are displayed when I try to do different actions within Bioconductor. Below are the error messages that I get when I perform the following actions ...

    • BiocManager::install()
    • Update all/some/none? [a/s/n]:
    • BiocManager::valid() # session info included
    • BiocManager::install("webchem", update = TRUE, ask = FALSE)
    • BiocManager::install("metaboliteIDmapping")

The problems seem to center around the Bioconductor repositories as it appears to be replacing the standard ones with a regular CRAN repository.

When I try to install packages, BC always declares that "package ‘XXXXX’ is available as a source package but not as a binary", but I can't compile the package successfully through the terminal. I try to install in the standard BC way (as below) or via the RStudio install packages feature.

BC always tries to update almost the same packages nearly every time I take an action whether I say ok to update or not.

Please advise.

Thanks, Jose


# 1. - BiocManager::install() =================================================================================================================

> if (!require("BiocManager", quietly = TRUE))
+     install.packages("BiocManager")
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)


> BiocManager::install()
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/bin/macosx/contrib/4.1:
  Found continuation line starting '    <script type="te ...' at begin of record.

---repeats 2x more

Warning: unable to access index for repository https://bioconductor.org/packages/3.14/books/bin/macosx/contrib/4.1:
  Found continuation line starting '    <script type="te ...' at begin of record.
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)

--- repeats 3x more

Warning: unable to access index for repository https://bioconductor.org/packages/3.14/books/bin/macosx/contrib/4.1:
  Found continuation line starting '    <script type="te ...' at begin of record.

Old packages: 'gmp', 'pander', 'parsnip', 'psych', 'psychTools', 'Rcpp', 'Rdpack', 'rncl', 'seriation', 'tidymodels', 'tune', 'workflows',
  'class', 'foreign', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet', 'rpart', 'spatial', 'survival'

# 2. - Update all/some/none? [a/s/n]:  ================================================================================================================

Update all/some/none? [a/s/n]: 
a
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/bin/macosx/contrib/4.1:
  Found continuation line starting '    <script type="te ...' at begin of record.

-- repeats 3x more

  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  859k  100  859k    0     0  3883k      0 --:--:-- --:--:-- --:--:-- 4093k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 1128k  100 1128k    0     0  5732k      0 --:--:-- --:--:-- --:--:-- 6101k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 1292k  100 1292k    0     0  4578k      0 --:--:-- --:--:-- --:--:-- 4786k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 4056k  100 4056k    0     0  10.7M      0 --:--:-- --:--:-- --:--:-- 11.1M
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 3501k  100 3501k    0     0  10.9M      0 --:--:-- --:--:-- --:--:-- 11.5M
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 3242k  100 3242k    0     0  9967k      0 --:--:-- --:--:-- --:--:-- 10.2M
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  726k  100  726k    0     0  4194k      0 --:--:-- --:--:-- --:--:-- 4599k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 4882k  100 4882k    0     0  13.4M      0 --:--:-- --:--:-- --:--:-- 13.9M
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 1154k  100 1154k    0     0  5056k      0 --:--:-- --:--:-- --:--:-- 5421k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  110k  100  110k    0     0   810k      0 --:--:-- --:--:-- --:--:--  912k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 1577k  100 1577k    0     0  7248k      0 --:--:-- --:--:-- --:--:-- 7731k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  209k  100  209k    0     0  1573k      0 --:--:-- --:--:-- --:--:-- 1760k

The downloaded binary packages are in
    /var/folders/58/7p64y9zj067d9sj5md9s1v6h0000gp/T//RtmpbvP24l/downloaded_packages
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 96398  100 96398    0     0   690k      0 --:--:-- --:--:-- --:--:--  778k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  323k  100  323k    0     0  1085k      0 --:--:-- --:--:-- --:--:-- 1144k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 1137k  100 1137k    0     0  4491k      0 --:--:-- --:--:-- --:--:-- 4738k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 5565k  100 5565k    0     0  7126k      0 --:--:-- --:--:-- --:--:-- 7265k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 3451k  100 3451k    0     0  7244k      0 --:--:-- --:--:-- --:--:-- 7471k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 2349k  100 2349k    0     0  9005k      0 --:--:-- --:--:-- --:--:-- 9551k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  126k  100  126k    0     0   923k      0 --:--:-- --:--:-- --:--:-- 1041k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  956k  100  956k    0     0  3624k      0 --:--:-- --:--:-- --:--:-- 3856k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  154k  100  154k    0     0  1256k      0 --:--:-- --:--:-- --:--:-- 1426k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 6875k  100 6875k    0     0  12.6M      0 --:--:-- --:--:-- --:--:-- 13.0M

The downloaded binary packages are in
    /var/folders/58/7p64y9zj067d9sj5md9s1v6h0000gp/T//RtmpbvP24l/downloaded_packages


# 3. - BiocManager::valid() =========================================================================================================================

> BiocManager::valid()     ## R version 3.5 or later
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories'
for details

replacement repositories:
    CRAN: https://cran.rstudio.com/


* sessionInfo()

R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.3

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

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

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

other attached packages:
[1] BiocManager_1.30.16

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8.3        tidyr_1.2.0         prettyunits_1.1.1   assertthat_0.2.1   
 [5] digest_0.6.29       packrat_0.7.0       utf8_1.2.2          mime_0.12          
 [9] BiocFileCache_2.2.1 R6_2.5.1            plyr_1.8.6          RSQLite_2.2.10     
[13] evaluate_0.15       httr_1.4.2          pillar_1.7.0        rlang_1.0.2        
[17] progress_1.2.2      curl_4.3.2          rstudioapi_0.13     data.table_1.14.2  
[21] jquerylib_0.1.4     blob_1.2.2          rmarkdown_2.13      flexdashboard_0.5.2
[25] stringr_1.4.0       bit_4.0.4           shiny_1.7.1         compiler_4.1.2     
[29] httpuv_1.6.5        xfun_0.30           pkgconfig_2.0.3     askpass_1.1        
[33] htmltools_0.5.2     openssl_2.0.0       tidyselect_1.1.2    tibble_3.1.6       
[37] lgr_0.4.3           biodb_1.2.2         attempt_0.3.1       XML_3.99-0.9       
[41] fansi_1.0.2         crayon_1.5.0        dplyr_1.0.8         dbplyr_2.1.1       
[45] withr_2.5.0         later_1.3.0         rappdirs_0.3.3      jsonlite_1.8.0     
[49] xtable_1.8-4        lifecycle_1.0.1     DBI_1.1.2           magrittr_2.0.2     
[53] cli_3.2.0           stringi_1.7.6       cachem_1.0.6        neo4r_0.1.1        
[57] fs_1.5.2            promises_1.2.0.1    bslib_0.3.1         ellipsis_0.3.2     
[61] chk_0.8.0           filelock_1.0.2      generics_0.1.2      vctrs_0.3.8        
[65] tools_4.1.2         bit64_4.0.5         glue_1.6.2          purrr_0.3.4        
[69] hms_1.1.1           fastmap_1.1.0       yaml_2.3.5          biodbHmdb_1.0.3    
[73] memoise_2.0.1       knitr_1.37          sass_0.4.0         

Bioconductor version '3.14'

  * 0 packages out-of-date
  * 1 packages too new

create a valid installation with

  BiocManager::install("webchem", update = TRUE, ask = FALSE)

more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date

Warning message:
0 packages out-of-date; 1 packages too new 


# 4. - BiocManager::install("webchem", update = TRUE, ask = FALSE)=========================================================================================


> BiocManager::install("webchem", update = TRUE, ask = FALSE)
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories'
for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/bin/macosx/contrib/4.1:
  Found continuation line starting '    <script type="te ...' at begin of record.

 -- repeasts 3x more

Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)

-- repeats 4x more

Warning message:
package(s) not installed when version(s) same as current; use `force = TRUE` to
  re-install: 'webchem' 

> if (!require("BiocManager", quietly = TRUE))
+     install.packages("BiocManager")


# 5. - BiocManager::install("metaboliteIDmapping") ====================================================================================================

> BiocManager::install("metaboliteIDmapping")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories'
for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Warning message repeated 4x 

Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)
Installing package(s) 'metaboliteIDmapping'

   package ‘metaboliteIDmapping’ is available as a source package but not as a binary

 -- repeated 4x

Warning messages:
1: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/bin/macosx/contrib/4.1:
  Found continuation line starting '    <script type="te ...' at begin of record.
2: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/bin/macosx/contrib/4.1:
  Found continuation line starting '    <script type="te ...' at begin of record.
3: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/workflows/bin/macosx/contrib/4.1:
  Found continuation line starting '    <script type="te ...' at begin of record.
4: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/books/bin/macosx/contrib/4.1:
  Found continuation line starting '    <script type="te ...' at begin of record.
5: In .inet_warning(msg) :
  package ‘metaboliteIDmapping’ is not available as a binary package for Bioconductor version '3.14'

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
packages installation Bioconductor updating • 3.0k views
ADD COMMENT •
0
Entering edit mode

Here's more of similar crap I've seen upon trying installations! Help with how to fix this would be appreciated!!!

> setRepositories()
--- Please select repositories for use in this session ---


1: + CRAN
2:   BioC software
3:   BioC annotation
4:   BioC experiment
5:   R-Forge
6:   rforge.net
7: + rstudio

Enter one or more numbers separated by spaces and then ENTER, or 0 to cancel
1: 2 3
Warning: unable to access index for repository https://bioconductor.org/packages/3.13/data/annotation/bin/macosx/contrib/4.1:
  Found continuation line starting '    <script type="te ...' at begin of record.
Warning: unable to access index for repository https://bioconductor.org/packages/3.13/data/annotation/bin/macosx/contrib/4.1:
  Found continuation line starting '    <script type="te ...' at begin of record.

> install.packages("BridgeDbR")
Installing package into ‘/Users/josemorales/Dropbox/Work/CU/Projects/1_Phenomics/1_Scores/1_LYMPS/Files/BG/packrat/lib/x86_64-apple-darwin17.0/4.1.2’
(as ‘lib’ is unspecified)
Warning in install.packages :
  unable to access index for repository https://bioconductor.org/packages/3.13/data/annotation/bin/macosx/contrib/4.1:
  Found continuation line starting '    <script type="te ...' at begin of record.
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 2676k  100 2676k    0     0  6359k      0 --:--:-- --:--:-- --:--:-- 6527k

The downloaded binary packages are in
    /var/folders/58/7p64y9zj067d9sj5md9s1v6h0000gp/T//RtmpInfKod/downloaded_packages
ADD REPLY •
0
Entering edit mode

How did you install R?

Check Problem loading R packages on MacBook Pro, tl;dr, did you accidentally install R for the newer Mac M1 machines rather than the Intel one? As a recommendation, you already have an error under # 1. so rather than posting all these compilation logs you should focus on this and try to resolve it. Everything downstream is often a consequence of the toplevel error. Be sure to have R installed correctly and try again. There are precompiled binaries for most packages on Intel Mac so it should not bother with compilation most of the time while for M1 Macs it (afaik) always compiles due to lack of binaries.

ADD REPLY •
0
Entering edit mode

Hi ATpoint,

Thanks for your response. While I was pretty sure I didn't install R incorrectly (because I use the updateR package, so I don't make the choice of what to click), I checked my version information. This is what I found...

> version
               _                           
platform          x86_64-apple-darwin17.0     
arch              x86_64                      
os                darwin17.0                  
system            x86_64, darwin17.0          
status                                     
major             4                           
minor             1.2                         
year              2021                        
month             11                          
day               01                          
svn rev           81115                       
language          R                           
version.string    R version 4.1.2 (2021-11-01)
nickname          Bird Hippie

If I am not mistaken, the following platform information is relevant..

  • x86_64-apple-darwin17.0: macOS High Sierra. ---> Not M1
  • aarch64-apple-darwin20: macOS Big Sur on arm64.---> M1

Consequently, since my version information corresponds with the "Not M1" platform, I installed the correct version of R on my MacBook Pro. Therefore, I return to my original problem of Bioconductor package installations not working.

Folks have any ideas on what is wrong and how its fixed?

Thanks in advance...Jose

ADD REPLY •
0
Entering edit mode
@marcel-ramos-7325
Last seen 8 days ago
United States

Hi Jose, jose

AFAICT, we don't provide binaries for annotation packages therefore something like https://bioconductor.org/packages/3.13/data/annotation/bin/macosx/contrib/4.1 looks quite odd.

These issues may stem from version mismatches due to version mixing (using the setRepositories() function) and possible installation issues with the latest MacOs 12.3.

Our builders are running macOS 10.14.6 Mojave where these packages are tested. From personal experience, OS updates on Mac are a pain to configure. Thankfully, I don't have a Mac ;)

My recommendations are:

  • Consider installing the latest R version 4.1.3 and make sure you have the right one installed (the Intel version binary)
  • Do not use setRepositories() (unless you know what you're doing; in this case, Bioc 3.13 is quite old now and would not help)
  • Clean out your directory where you've installed mixed versions of packages. The easiest way to do this is to remove all the packages and start anew.

Please only use BiocManager::install to install packages that are appropriate to your R version.

Best regards,

Marcel
ADD COMMENT •
1
Entering edit mode

Ah Marcel!

Yes, indeed I have used setRepositories() in trying to install bioconductor packages! Given Monterey's newness, that would be a likely suspect as well.

I will indeed install the latest R version. Would there be any problem with my using the updateR package to do the update? I've used it before without any issues.

As for cleaning out the directory with mixed versions of packages...Yikes!

I will indeed ONLY use BiocManager::install from this point forward!

Thank you so much! Jose

ADD REPLY •
0
Entering edit mode

I recommend using the Mac binaries at https://cran.r-project.org/bin/macosx/ to update R.

That's what the Core team uses for the builders. We have not used updateR.

Best regards, Marcel

ADD REPLY •

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