packageVersion(“Maaslin2”)
[1] ‘1.13.0’
packageVersion(“lpsymphony”)
[1] ‘1.27.1’
I am trying to install Maaslin2 and run it. I am able to get this far:
if(!requireNamespace(“BiocManager”, quietly = TRUE))
- install.packages(“BiocManager”)
BiocManager::install(“Maaslin2”)
‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘help(“repositories”, package = “BiocManager”)’ for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21)
Old packages: ‘lpsymphony’
Update all/some/none? [a/s/n]:
a
trying URL ‘https://bioconductor.org/packages/3.17/bioc/bin/macosx/big-sur-x86_64/contrib/4.3/lpsymphony_1.27.1.tgz’
Content type ‘application/x-gzip’ length 2159400 bytes (2.1 MB)
==================================================
downloaded 2.1 MB
The downloaded binary packages are in
/var/folders/fv/z5nqrkvn1kgcppzkw1vyll1w0000gn/T//RtmpF4nAUc/downloaded_packages
Warning message:
package(s) not installed when version(s) same as or greater than current; use force = TRUE to re-install: ‘Maaslin2’
Then when I go to install Maaslin2 I get the following issue with loading lpsymphony:
library(Maaslin2)
Error: package or namespace load failed for ‘Maaslin2’ in dyn.load(file, DLLpath = DLLpath, …):
unable to load shared object ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/lpsymphony/libs/lpsymphony.so’:
dlopen(/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/lpsymphony/libs/lpsymphony.so, 0x0006): Library not loaded: /Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libRlapack.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/lpsymphony/libs/lpsymphony.so
Reason: tried: ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libRlapack.dylib’ (no such file), ‘/System/Volumes/Preboot/Cryptexes/OS/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libRlapack.dylib’ (no such file), ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libRlapack.dylib’ (no such file), ‘/usr/local/lib/libRlapack.dylib’ (no such file), '/usr/l
I’ve even tried this to get to the bottom of the issue:
if (!require(“BiocManager”, quietly = TRUE))
- install.packages(“BiocManager”)
pkgs ← rownames(installed.packages())
BiocManager::install(pkgs, type = “source”, checkBuilt = TRUE)
It appears there is a compilation issue with lpsymphony
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make[4]: *** [CoinBuild.lo] Error 1
make[3]: *** [all] Error 2
make[2]: *** [all-recursive] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [SYMPHONY.ts] Error 2
ERROR: compilation failed for package ‘lpsymphony’
-
removing ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/lpsymphony’
-
restoring previous ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/lpsymphony’
The downloaded source packages are in
‘/private/var/folders/fv/z5nqrkvn1kgcppzkw1vyll1w0000gn/T/RtmpyLCDhb/downloaded_packages’
Old packages: ‘lpsymphony’
Update all/some/none? [a/s/n]:
a
trying URL ‘https://bioconductor.org/packages/3.17/bioc/src/contrib/lpsymphony_1.28.0.tar.gz’
Content type ‘application/x-gzip’ length 12417432 bytes (11.8 MB)
==================================================
downloaded 11.8 MB
- installing source package ‘lpsymphony’ …
** using staged installation
- Defaulting to clang/clang++
Which then ends like this:
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make[4]: *** [CoinBuild.lo] Error 1
make[3]: *** [all] Error 2
make[2]: *** [all-recursive] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [SYMPHONY.ts] Error 2
ERROR: compilation failed for package ‘lpsymphony’
-
removing ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/lpsymphony’
-
restoring previous ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/lpsymphony’
The downloaded source packages are in
‘/private/var/folders/fv/z5nqrkvn1kgcppzkw1vyll1w0000gn/T/RtmpyLCDhb/downloaded_packages’
Warning messages:
1: package(s) not installed when version(s) same as or greater than current; use force = TRUE to re-install: ‘abind’ ‘askpass’ ‘backports’
‘base’ ‘base64enc’ ‘biglm’ ‘Biobase’ ‘BiocGenerics’ ‘BiocManager’ ‘BiocVersion’ ‘bitops’ ‘boot’ ‘brew’ ‘brio’ ‘broom’ ‘bslib’ ‘cachem’
‘callr’ ‘car’ ‘carData’ ‘caTools’ ‘chemometrics’ ‘class’ ‘cli’ ‘clipr’ ‘cluster’ ‘coda’ ‘codetools’ ‘colorspace’ ‘commonmark’ ‘compiler’
‘cowplot’ ‘cplm’ ‘cpp11’ ‘crayon’ ‘credentials’ ‘curl’ ‘data.table’ ‘datasets’ ‘DBI’ ‘DEoptimR’ ‘desc’ ‘devtools’ ‘diffobj’ ‘digest’
‘downlit’ ‘dplyr’ ‘e1071’ ‘edgeR’ ‘ellipsis’ ‘evaluate’ ‘fansi’ ‘farver’ ‘fastmap’ ‘fontawesome’ ‘foreach’ ‘foreign’ ‘fs’ ‘generics’ ‘gert’
‘getopt’ ‘ggplot2’ ‘gh’ ‘gitcreds’ ‘glmmTMB’ ‘glmnet’ ‘glue’ ‘gplots’ ‘graphics’ ‘grDevices’ ‘grid’ ‘gridExtra’ ‘gtable’ ‘gtools’ ‘hash’
‘highr’ ‘htmltools’ ‘htmlwidgets’ ‘httpuv’ ‘httr’ ‘httr2’ ‘ini’ ‘isoband’ ‘iterators’ ‘jquerylib’ ‘jsonlite’ ‘KernSmooth’ ‘knitr’ ‘labeling’
‘lars’ ‘later’ ‘lattice’ [… truncated]
2: In install.packages(…) :
installation of package ‘lpsymphony’ had non-zero exit status
3: In install.packages(update[instlib == l, “Package”], l, contriburl = contriburl, :
installation of package ‘lpsymphony’ had non-zero exit status
What can I do to fix the lpsymphony installation?
Running BiocManager::install(‘lpsymphony’) does not seem to fix anything.
Thanks!
Diana