BiocManager::install("goseq")
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.1 (2023-06-16)
Installing package(s) 'goseq'
also installing the dependencies ‘SparseArray’, ‘MatrixGenerics’, ‘DelayedArray’, ‘SummarizedExperiment’, ‘GenomicAlignments’, ‘restfulr’, ‘biomaRt’, ‘rtracklayer’, ‘GenomicFeatures’, ‘KEGGREST’, ‘geneLenDataBase’, ‘AnnotationDbi’, ‘GO.db’
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/SparseArray_1.2.4.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/MatrixGenerics_1.14.0.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/DelayedArray_0.28.0.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/SummarizedExperiment_1.32.0.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/GenomicAlignments_1.38.2.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/GenomicFeatures_1.54.3.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/KEGGREST_1.42.0.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.18/data/experiment/src/contrib/geneLenDataBase_1.38.0.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GO.db_3.18.0.tar.gz'
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* installing *source* package ‘MatrixGenerics’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ‘matrixStats’:
package ‘matrixStats’ was installed before R 4.0.0: please re-install it
Execution halted
ERROR: lazy loading failed for package ‘MatrixGenerics’
* removing ‘/tscc/nfs/home/ekunselm/miniconda3/envs/trinity/lib/R/library/MatrixGenerics’
* installing *source* package ‘restfulr’ ...
** package ‘restfulr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘x86_64-conda-linux-gnu-cc (Anaconda gcc) 11.2.0’
x86_64-conda-linux-gnu-cc -I"/tscc/nfs/home/ekunselm/miniconda3/envs/trinity/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /tscc/nfs/home/ekunselm/miniconda3/envs/trinity/include -I/tscc/nfs/home/ekunselm/miniconda3/envs/trinity/include -Wl,-rpath-link,/tscc/nfs/home/ekunselm/miniconda3/envs/trinity/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /tscc/nfs/home/ekunselm/miniconda3/envs/trinity/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/tscc/nfs/home/ekunselm/miniconda3/envs/trinity=/usr/local/src/conda-prefix -c init.c -o init.o
x86_64-conda-linux-gnu-cc -I"/tscc/nfs/home/ekunselm/miniconda3/envs/trinity/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /tscc/nfs/home/ekunselm/miniconda3/envs/trinity/include -I/tscc/nfs/home/ekunselm/miniconda3/envs/trinity/include -Wl,-rpath-link,/tscc/nfs/home/ekunselm/miniconda3/envs/trinity/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /tscc/nfs/home/ekunselm/miniconda3/envs/trinity/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/tscc/nfs/home/ekunselm/miniconda3/envs/trinity=/usr/local/src/conda-prefix -c raggedListToDF.c -o raggedListToDF.o
x86_64-conda-linux-gnu-cc -shared -L/tscc/nfs/home/ekunselm/miniconda3/envs/trinity/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/tscc/nfs/home/ekunselm/miniconda3/envs/trinity/lib -Wl,-rpath-link,/tscc/nfs/home/ekunselm/miniconda3/envs/trinity/lib -L/tscc/nfs/home/ekunselm/miniconda3/envs/trinity/lib -o restfulr.so init.o raggedListToDF.o -L/tscc/nfs/home/ekunselm/miniconda3/envs/trinity/lib/R/lib -lR
installing to /tscc/nfs/home/ekunselm/miniconda3/envs/trinity/lib/R/library/00LOCK-restfulr/00new/restfulr/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package ‘RCurl’ was installed before R 4.0.0: please re-install it
Execution halted
ERROR: lazy loading failed for package ‘restfulr’
* removing ‘/tscc/nfs/home/ekunselm/miniconda3/envs/trinity/lib/R/library/restfulr’
* installing *source* package ‘KEGGREST’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package ‘httr’ was installed before R 4.0.0: please re-install it
Execution halted
ERROR: lazy loading failed for package ‘KEGGREST’
* removing ‘/tscc/nfs/home/ekunselm/miniconda3/envs/trinity/lib/R/library/KEGGREST’
ERROR: dependency ‘MatrixGenerics’ is not available for package ‘SparseArray’
* removing ‘/tscc/nfs/home/ekunselm/miniconda3/envs/trinity/lib/R/library/SparseArray’
ERROR: dependency ‘KEGGREST’ is not available for package ‘AnnotationDbi’
* removing ‘/tscc/nfs/home/ekunselm/miniconda3/envs/trinity/lib/R/library/AnnotationDbi’
ERROR: dependencies ‘MatrixGenerics’, ‘SparseArray’ are not available for package ‘DelayedArray’
* removing ‘/tscc/nfs/home/ekunselm/miniconda3/envs/trinity/lib/R/library/DelayedArray’
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘biomaRt’
* removing ‘/tscc/nfs/home/ekunselm/miniconda3/envs/trinity/lib/R/library/biomaRt’
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘GO.db’
* removing ‘/tscc/nfs/home/ekunselm/miniconda3/envs/trinity/lib/R/library/GO.db’
ERROR: dependencies ‘MatrixGenerics’, ‘DelayedArray’ are not available for package ‘SummarizedExperiment’
* removing ‘/tscc/nfs/home/ekunselm/miniconda3/envs/trinity/lib/R/library/SummarizedExperiment’
ERROR: dependency ‘SummarizedExperiment’ is not available for package ‘GenomicAlignments’
* removing ‘/tscc/nfs/home/ekunselm/miniconda3/envs/trinity/lib/R/library/GenomicAlignments’
ERROR: dependencies ‘GenomicAlignments’, ‘restfulr’ are not available for package ‘rtracklayer’
* removing ‘/tscc/nfs/home/ekunselm/miniconda3/envs/trinity/lib/R/library/rtracklayer’
ERROR: dependencies ‘AnnotationDbi’, ‘rtracklayer’, ‘biomaRt’ are not available for package ‘GenomicFeatures’
* removing ‘/tscc/nfs/home/ekunselm/miniconda3/envs/trinity/lib/R/library/GenomicFeatures’
ERROR: dependencies ‘rtracklayer’, ‘GenomicFeatures’ are not available for package ‘geneLenDataBase’
* removing ‘/tscc/nfs/home/ekunselm/miniconda3/envs/trinity/lib/R/library/geneLenDataBase’
ERROR: dependencies ‘geneLenDataBase’, ‘AnnotationDbi’, ‘GO.db’ are not available for package ‘goseq’
* removing ‘/tscc/nfs/home/ekunselm/miniconda3/envs/trinity/lib/R/library/goseq’
The downloaded source packages are in
‘/tmp/RtmpNeNz4z/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Old packages: 'BiocFileCache'
Update all/some/none? [a/s/n]: n
There were 14 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: In install.packages(...) :
installation of package ‘MatrixGenerics’ had non-zero exit status
2: In install.packages(...) :
installation of package ‘restfulr’ had non-zero exit status
3: In install.packages(...) :
installation of package ‘KEGGREST’ had non-zero exit status
4: In install.packages(...) :
installation of package ‘SparseArray’ had non-zero exit status
5: In install.packages(...) :
installation of package ‘AnnotationDbi’ had non-zero exit status
6: In install.packages(...) :
installation of package ‘DelayedArray’ had non-zero exit status
7: In install.packages(...) :
installation of package ‘biomaRt’ had non-zero exit status
8: In install.packages(...) :
installation of package ‘GO.db’ had non-zero exit status
9: In install.packages(...) :
installation of package ‘SummarizedExperiment’ had non-zero exit status
10: In install.packages(...) :
installation of package ‘GenomicAlignments’ had non-zero exit status
11: In install.packages(...) :
installation of package ‘rtracklayer’ had non-zero exit status
12: In install.packages(...) :
installation of package ‘GenomicFeatures’ had non-zero exit status
13: In install.packages(...) :
installation of package ‘geneLenDataBase’ had non-zero exit status
14: In install.packages(...) :
installation of package ‘goseq’ had non-zero exit status
> sessionInfo( )
R version 4.3.1 (2023-06-16)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Rocky Linux 9.2 (Blue Onyx)
Matrix products: default
BLAS/LAPACK: /tscc/nfs/home/ekunselm/miniconda3/envs/trinity/lib/libopenblasp-r0.3.21.so; LAPACK version 3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: America/Los_Angeles
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] BiocManager_1.30.22 compiler_4.3.1 tools_4.3.1
Error: Error, missing gene lengths for features: TRINITY_DN3434_c0_g1_i1, TRINITY_DN4332_c1_g1_i14, TRINITY_DN997_c2_g1_i1, TRINITY_DN6518_c0_g1_i2, TRINITY_DN3781_c2_g1_i2, TRINITY_DN5538_c2_g1_i8, TRINITY_DN1553_c0_g1_i40, TRINITY_DN11842_c0_g1_i16, TRINITY_DN2325_c0_g1_i2, TRINITY_DN1285_c0_g1_i8, TRINITY_DN1151_c11_g1_i1, TRINITY_DN11518_c3_g1_i2, TRINITY_DN1234_c6_g1_i1, TRINITY_DN25060_c0_g1_i20, TRINITY_DN1485_c1_g1_i4, TRINITY_DN6475_c2_g2_i2, TRINITY_DN6068_c3_g1_i2, TRINITY_DN786_c0_g1_i3, TRINITY_DN1316_c0_g1_i8, TRINITY_DN6823_c14_g2_i2, TRINITY_DN18671_c0_g2_i35, TRINITY_DN5473_c0_g1_i23, TRINITY_DN62477_c1_g3_i2, TRINITY_DN54974_c0_g1_i3, TRINITY_DN4809_c0_g1_i2, TRINITY_DN1059_c0_g1_i7, TRINITY_DN4308_c0_g2_i1, TRINITY_DN24048_c0_g1_i1, TRINITY_DN15683_c0_g1_i1, TRINITY_DN45414_c0_g1_i59, TRINITY_DN17892_c0_g1_i12, TRINITY_DN95777_c1_g1_i1, TRINITY_DN79707_c0_g1_i6, TRINITY_DN1812_c2_g1_i3, TRINITY_DN2728_c0_g1_i5, TRINITY_DN1147_c0_g1_i8, TRINITY_DN3848_c0_g1_i3, TRINIT
Execution halted
Error, cmd: R --no-save --no-restore --no-site-file --no-init-file --quiet < __runGOseq.R died with ret 256 at /tscc/nfs/home/ekunselm/miniconda3/envs/trinity/opt/trinity-2.8.5/Analysis/DifferentialExpression/run_GOseq.pl line 197.
Warning, go-seq failed for Trinity_trans.isoform.counts.matrix.Control_vs_Exposed.edgeR.DE_results.P1e-3_C2.DE.subset: Error, cmd: /tscc/nfs/home/ekunselm/miniconda3/envs/trinity/opt/trinity-2.8.5/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments ../go_annotations.txt --lengths ../Trinity.gene_lengths.txt --genes_single_factor Trinity_trans.isoform.counts.matrix.Control_vs_Exposed.edgeR.DE_results.P1e-3_C2.DE.subset --background Trinity_trans.isoform.counts.matrix.Control_vs_Exposed.edgeR.count_matrix died with ret 6400 at /tscc/nfs/home/ekunselm/miniconda3/envs/trinity/bin/analyze_diff_expr.pl line 272.
```
But I am not sure why this is the case because I ran...
trinityrnaseq-v2.15.1/util/misc/TPM_weighted_gene_length.py \
--gene_trans_map Trinity.fasta.gene_trans_map \
--trans_lengths Trinity.fasta.seq_lens \
--TPM_matrix Trinity_trans.isoform.TMM.EXPR.matrix > Trinity.gene_lengths.txt
...with no issues.
Any help is greatly appreciated,
Emily