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lina.bird
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@linabird-23441
Last seen 4.7 years ago
I am trying to install the package pcaExplorer. Code is below. It seems like GenomeInfoDbData is the problem, but I'm not clear on how to fix it. I've tried installing it directly, and it gives me the "Installation path not writable". I am running R 4.0.0, and do not have admin privileges on my computer.
BiocManager::install("pcaExplorer")
I get the following errors:
dyld: lazy symbol binding failed: Symbol not found: _utimensat
Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13)
Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: _utimensat
Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13)
Expected in: /usr/lib/libSystem.B.dylib
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 57689 Done echo 'tools:::.install_packages()'
57690 Abort trap: 6 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}
The downloaded source packages are in
‘/private/var/folders/4p/qfhkb73d5v18fx4t14hkhqz8j80qs4/T/RtmpiVryPm/downloaded_packages’
Installation path not writeable, unable to update packages: boot, class,
foreign, KernSmooth, MASS, nnet, spatial
Warning message:
In install.packages(...) :
installation of package ‘GO.db’ had non-zero exit status
When I try to load it:
library(pcaExplorer)
Error: package or namespace load failed for ‘pcaExplorer’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘GenomeInfoDbData’
sessionInfo results:
R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Sierra 10.12.5
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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
loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_4.0.0 IRanges_2.21.8
[4] parallel_4.0.0 tools_4.0.0 RCurl_1.98-1.2
[7] Biobase_2.47.3 S4Vectors_0.25.15 BiocGenerics_0.33.3
[10] BiocParallel_1.21.3 bitops_1.0-6 stats4_4.0.0
Any suggestions would be appreciated.
Yes. it is too long, here are the parts with issues. I am running Mac OS X 10.12.5; is that a problem?
dyld: lazy symbol binding failed: Symbol not found: _utimensat Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Expected in: /usr/lib/libSystem.B.dylib
The downloaded source packages are in ‘/private/var/folders/4p/qfhkb73d5v18fx4t14hkhqz8j80qs4/T/RtmpiVryPm/downloaded_packages’ Installation path not writeable, unable to update packages: boot, class, foreign, KernSmooth, MASS, nnet, spatial Old packages: 'annotate', 'AnnotationDbi', 'AnnotationForge', 'Biobase', 'BiocFileCache', 'BiocGenerics', 'BiocParallel', 'biomaRt', 'Category', 'DelayedArray', 'DESeq2', 'genefilter', 'geneplotter', 'GenomeInfoDb', 'GenomicRanges', 'GOstats', 'graph', 'GSEABase', 'IRanges', 'limma', 'pcaExplorer', 'RBGL', 'Rgraphviz', 'S4Vectors', 'SummarizedExperiment', 'topGO', 'XVector', 'zlibbioc' Update all/some/none? [a/s/n]: a also installing the dependencies ‘RcppArmadillo’, ‘GenomeInfoDbData’, ‘GO.db’
Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes
The downloaded binary packages are in /var/folders/4p/qfhkb73d5v18fx4t14hkhqz8j80qs4/T//RtmpiVryPm/downloaded_packages installing the source packages ‘RcppArmadillo’, ‘GenomeInfoDbData’, ‘GO.db’, ‘annotate’
dyld: lazy symbol binding failed: Symbol not found: _utimensat Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: _utimensat Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Expected in: /usr/lib/libSystem.B.dylib
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 65724 Done echo 'tools:::.installpackages()' 65725 Abort trap: 6 | RDEFAULTPACKAGES= LCCOLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args} dyld: lazy symbol binding failed: Symbol not found: _utimensat Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: _utimensat Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Expected in: /usr/lib/libSystem.B.dylib
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 65733 Done echo 'tools:::.installpackages()' 65734 Abort trap: 6 | RDEFAULTPACKAGES= LCCOLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args} dyld: lazy symbol binding failed: Symbol not found: _utimensat Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: _utimensat Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Expected in: /usr/lib/libSystem.B.dylib
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 65742 Done echo 'tools:::.installpackages()' 65743 Abort trap: 6 | RDEFAULTPACKAGES= LCCOLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args} dyld: lazy symbol binding failed: Symbol not found: _utimensat Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: _utimensat Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Expected in: /usr/lib/libSystem.B.dylib
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 65752 Done echo 'tools:::.installpackages()' 65753 Abort trap: 6 | RDEFAULTPACKAGES= LCCOLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}
Warning messages: 1: In install.packages(...) : installation of package ‘GenomeInfoDbData’ had non-zero exit status 2: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ‘RcppArmadillo’ had non-zero exit status 3: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ‘GenomeInfoDbData’ had non-zero exit status 4: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ‘GO.db’ had non-zero exit status 5: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ‘annotate’ had non-zero exit status