Entering edit mode
5 weeks ago
Nitin
•
0
Hello,
I am trying to analyze the single cell seq results using Bioconductor packages in Posit Workbench. one of the requirement is load the library "scater', for this I am trying to load the package as mentioned here: https://bioconductor.org/packages/release/bioc/html/scater.html
here is the error
'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 1.30.22), R 4.3.3 (2024-02-29)
Installing package(s) 'scater'
also installing the dependency ‘densvis’
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/bin/macosx/big-sur-arm64/contrib/4.3:
cannot open URL 'https://bioconductor.org/packages/3.17/data/annotation/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/bin/macosx/big-sur-arm64/contrib/4.3:
cannot open URL 'https://bioconductor.org/packages/3.17/data/experiment/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/workflows/bin/macosx/big-sur-arm64/contrib/4.3:
cannot open URL 'https://bioconductor.org/packages/3.17/workflows/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES'
Package which is only available in source form, and may need compilation of C/C++/Fortran:
‘densvis’
Do you want to attempt to install these from sources? (Yes/no/cancel) Yes
installing the source packages ‘densvis’, ‘scater’
trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/densvis_1.10.3.tar.gz'
Content type 'application/gzip' length 1731202 bytes (1.7 MB)
==================================================
downloaded 1.7 MB
trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/scater_1.28.0.tar.gz'
Content type 'application/gzip' length 4089325 bytes (3.9 MB)
==================================================
downloaded 3.9 MB
* installing *source* package ‘densvis’ ...
** using non-staged installation via StagedInstall field
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.3.9.4)’
using C++14
using SDK: ‘MacOSX14.4.sdk’
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c densne.cpp -o densne.o
densne.cpp:181:24: warning: variable 'row_P' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized]
for(int i = 0; i < N * N; i++) P[i] /= sum_P;
^~~~~~~~~
densne.cpp:201:33: note: uninitialized use occurs here
computeExpectedLogDist(&ro, row_P, col_P, val_P, val_D, N, logdist_shift);
^~~~~
densne.cpp:181:24: note: remove the condition if it is always true
for(int i = 0; i < N * N; i++) P[i] /= sum_P;
^~~~~~~~~
densne.cpp:154:35: note: initialize the variable 'row_P' to silence this warning
double* P; unsigned int* row_P; unsigned int* col_P; double* val_P; double* val_D;
^
= nullptr
densne.cpp:181:24: warning: variable 'col_P' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized]
for(int i = 0; i < N * N; i++) P[i] /= sum_P;
^~~~~~~~~
densne.cpp:201:40: note: uninitialized use occurs here
computeExpectedLogDist(&ro, row_P, col_P, val_P, val_D, N, logdist_shift);
^~~~~
densne.cpp:181:24: note: remove the condition if it is always true
for(int i = 0; i < N * N; i++) P[i] /= sum_P;
^~~~~~~~~
densne.cpp:154:56: note: initialize the variable 'col_P' to silence this warning
double* P; unsigned int* row_P; unsigned int* col_P; double* val_P; double* val_D;
^
= nullptr
densne.cpp:181:24: warning: variable 'val_P' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized]
for(int i = 0; i < N * N; i++) P[i] /= sum_P;
^~~~~~~~~
densne.cpp:201:47: note: uninitialized use occurs here
computeExpectedLogDist(&ro, row_P, col_P, val_P, val_D, N, logdist_shift);
^~~~~
densne.cpp:181:24: note: remove the condition if it is always true
for(int i = 0; i < N * N; i++) P[i] /= sum_P;
^~~~~~~~~
densne.cpp:154:71: note: initialize the variable 'val_P' to silence this warning
double* P; unsigned int* row_P; unsigned int* col_P; double* val_P; double* val_D;
^
= nullptr
densne.cpp:181:24: warning: variable 'val_D' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized]
for(int i = 0; i < N * N; i++) P[i] /= sum_P;
^~~~~~~~~
densne.cpp:201:54: note: uninitialized use occurs here
computeExpectedLogDist(&ro, row_P, col_P, val_P, val_D, N, logdist_shift);
^~~~~
densne.cpp:181:24: note: remove the condition if it is always true
for(int i = 0; i < N * N; i++) P[i] /= sum_P;
^~~~~~~~~
densne.cpp:154:86: note: initialize the variable 'val_D' to silence this warning
double* P; unsigned int* row_P; unsigned int* col_P; double* val_P; double* val_D;
^
= nullptr
4 warnings generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c densvis.cpp -o densvis.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sptree.cpp -o sptree.o
clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o densvis.so RcppExports.o densne.o densvis.o sptree.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: search path '/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0' not found
ld: warning: search path '/opt/gfortran/lib' not found
ld: library 'gfortran' not found
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [densvis.so] Error 1
ERROR: compilation failed for package ‘densvis’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/densvis’
ERROR: dependency ‘densvis’ is not available for package ‘scater’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/scater’
The downloaded source packages are in
‘/private/var/folders/tz/nsfls9s119lghfj59y3fd0300000gn/T/RtmpUgVfB6/downloaded_packages’
Old packages: 'clustermole'
Update all/some/none? [a/s/n]:
a
Warning: dependency ‘GSVA (>= 1.50.0)’ is not available
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/bin/macosx/big-sur-arm64/contrib/4.3:
cannot open URL 'https://bioconductor.org/packages/3.17/data/annotation/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/bin/macosx/big-sur-arm64/contrib/4.3:
cannot open URL 'https://bioconductor.org/packages/3.17/data/experiment/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/workflows/bin/macosx/big-sur-arm64/contrib/4.3:
cannot open URL 'https://bioconductor.org/packages/3.17/workflows/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES'
installing the source package ‘clustermole’
my session Info
sessionInfo()
R version 4.3.3 (2024-02-29)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.4
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Chicago
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1
[4] purrr_1.0.2 readr_2.1.5 tidyr_1.3.1
[7] tibble_3.2.1 tidyverse_2.0.0 speckle_1.0.0
[10] pbmcsca.SeuratData_3.0.0 pbmcref.SeuratData_1.0.0 SeuratData_0.2.2.9001
[13] Seurat_5.0.3 SeuratObject_5.0.1 sp_2.1-3
[16] scran_1.28.2 scuttle_1.10.3 SingleCellExperiment_1.24.0
[19] SummarizedExperiment_1.32.0 GenomicRanges_1.54.1 GenomeInfoDb_1.38.5
[22] MatrixGenerics_1.14.0 matrixStats_1.2.0 patchwork_1.2.0.9000
[25] paletteer_1.6.0 org.Hs.eg.db_3.17.0 AnnotationDbi_1.64.1
[28] IRanges_2.36.0 S4Vectors_0.40.2 Biobase_2.62.0
[31] BiocGenerics_0.48.1 miQC_1.8.0 limma_3.56.2
[34] ggpubr_0.6.0.999 glmGamPoi_1.14.0 dplyr_1.1.4
[37] DoubletFinder_2.0.3 data.table_1.15.2 cowplot_1.1.3
[40] clustree_0.5.1 ggraph_2.2.1 ggplot2_3.5.0
[43] BiocManager_1.30.22
loaded via a namespace (and not attached):
[1] spatstat.sparse_3.0-3 bitops_1.0-7 httr_1.4.7
[4] RColorBrewer_1.1-3 tools_4.3.3 sctransform_0.4.1
[7] backports_1.4.1 utf8_1.2.4 R6_2.5.1
[10] lazyeval_0.2.2 uwot_0.1.16 withr_3.0.0
[13] gridExtra_2.3 progressr_0.14.0 cli_3.6.2
[16] pacman_0.5.1 spatstat.explore_3.2-6 fastDummies_1.7.3
[19] spatstat.data_3.0-4 ggridges_0.5.6 pbapply_1.7-2
[22] parallelly_1.37.1 rstudioapi_0.15.0 RSQLite_2.3.5
[25] generics_0.1.3 ica_1.0-3 spatstat.random_3.2-3
[28] car_3.1-2 Matrix_1.6-5 fansi_1.0.6
[31] abind_1.4-5 lifecycle_1.0.4 edgeR_3.42.4
[34] carData_3.0-5 SparseArray_1.2.3 Rtsne_0.17
[37] grid_4.3.3 blob_1.2.4 promises_1.2.1
[40] dqrng_0.3.2 crayon_1.5.2 miniUI_0.1.1.1
[43] lattice_0.22-5 beachmat_2.18.0 KEGGREST_1.42.0
[46] pillar_1.9.0 knitr_1.45 metapod_1.8.0
[49] future.apply_1.11.1 codetools_0.2-19 leiden_0.4.3.1
[52] glue_1.7.0 vctrs_0.6.5 png_0.1-8
[55] spam_2.10-0 gtable_0.3.4 rematch2_2.1.2
[58] cachem_1.0.8 xfun_0.42 S4Arrays_1.2.0
[61] mime_0.12 tidygraph_1.3.1 survival_3.5-8
[64] statmod_1.5.0 bluster_1.10.0 ellipsis_0.3.2
[67] fitdistrplus_1.1-11 ROCR_1.0-11 nlme_3.1-164
[70] bit64_4.0.5 RcppAnnoy_0.0.22 irlba_2.3.5.1
[73] KernSmooth_2.23-22 colorspace_2.1-0 DBI_1.2.2
[76] nnet_7.3-19 tidyselect_1.2.1 bit_4.0.5
[79] compiler_4.3.3 BiocNeighbors_1.18.0 DelayedArray_0.28.0
[82] plotly_4.10.4 scales_1.3.0 lmtest_0.9-40
[85] rappdirs_0.3.3 digest_0.6.35 goftest_1.2-3
[88] spatstat.utils_3.0-4 XVector_0.42.0 htmltools_0.5.7
[91] pkgconfig_2.0.3 sparseMatrixStats_1.14.0 fastmap_1.1.1
[94] rlang_1.1.3 htmlwidgets_1.6.4 shiny_1.8.0
[97] DelayedMatrixStats_1.24.0 farver_2.1.1 zoo_1.8-12
[100] jsonlite_1.8.8 BiocParallel_1.36.0 BiocSingular_1.16.0
[103] RCurl_1.98-1.14 magrittr_2.0.3 modeltools_0.2-23
[106] GenomeInfoDbData_1.2.11 dotCall64_1.1-1 munsell_0.5.0
[109] Rcpp_1.0.12 viridis_0.6.5 reticulate_1.35.0
[112] stringi_1.8.3 zlibbioc_1.48.0 MASS_7.3-60.0.1
[115] plyr_1.8.9 flexmix_2.3-19 parallel_4.3.3
[118] listenv_0.9.1 ggrepel_0.9.5 deldir_2.0-4
[121] Biostrings_2.70.1 graphlayouts_1.1.1 splines_4.3.3
[124] tensor_1.5 hms_1.1.3 locfit_1.5-9.9
[127] igraph_2.0.3 spatstat.geom_3.2-9 ggsignif_0.6.4
[130] RcppHNSW_0.6.0 reshape2_1.4.4 ScaledMatrix_1.8.1
[133] tzdb_0.4.0 tweenr_2.0.3 httpuv_1.6.14
[136] RANN_2.6.1 polyclip_1.10-6 future_1.33.1
[139] scattermore_1.2 ggforce_0.4.2 rsvd_1.0.5
[142] broom_1.0.5 xtable_1.8-4 RSpectra_0.16-1
[145] rstatix_0.7.2 later_1.3.2 viridisLite_0.4.2
[148] memoise_2.0.1 cluster_2.1.6 timechange_0.3.0
[151] globals_0.16.3
I urge you to read back what you wrote and think whether you'd be able to help someone who gave you this little information. If I said that I couldn't make a French toast without telling you any details, would you be able to help me?
I've merged your posts but in the future, please add comments unless you're actually answering the top level question.
I don't think ARM R + bioconductor is 100% robust yet. For the moment, to have a reliable environment, install and use intel R.