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
Here's more of similar crap I've seen upon trying installations! Help with how to fix this would be appreciated!!!
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.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...
If I am not mistaken, the following platform information is relevant..
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