Error when installing pcaExplorer
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lina.bird • 0
@linabird-23441
Last seen 13 months 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.

install GenomeInfoDbData • 138 views
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@james-w-macdonald-5106
Last seen 1 hour ago
United States

Did you try BiocManager::install("GenomeInfoDbData")?

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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

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