issue installing goseq in R for use with analyze_diff_expr.pl

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Emily Kunselman

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Mar 7, 2024, 2:39:37 PMMar 7
to trinityrnaseq-users
Hello,

I am trying to run analyze_diff_expr.pl with go annotations as follows:

analyze_diff_expr.pl --matrix ../Trinity_trans.isoform.TMM.EXPR.matrix -P 1e-3 -C 2 --samples edgeR_sample_identifiers.txt --order_columns_by_samples_file --examine_GO_enrichment --GO_annots go_annotations.txt --gene_lengths Trinity.gene_lengths.txt --include_GOplot

But I am having an issue in R because there is no goseq package, among others. So, I tried to install goseq with BiocManager::install("goseq") but I get the following error:

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'

Content type 'application/x-gzip' length 367778 bytes (359 KB)

==================================================

downloaded 359 KB


trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/MatrixGenerics_1.14.0.tar.gz'

Content type 'application/x-gzip' length 31230 bytes (30 KB)

==================================================

downloaded 30 KB


trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/DelayedArray_0.28.0.tar.gz'

Content type 'application/x-gzip' length 624166 bytes (609 KB)

==================================================

downloaded 609 KB


trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/SummarizedExperiment_1.32.0.tar.gz'

Content type 'application/x-gzip' length 686052 bytes (669 KB)

==================================================

downloaded 669 KB


trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/GenomicAlignments_1.38.2.tar.gz'

Content type 'application/x-gzip' length 2265818 bytes (2.2 MB)

==================================================

downloaded 2.2 MB


trying URL 'https://cloud.r-project.org/src/contrib/restfulr_0.0.15.tar.gz'

Content type 'application/x-gzip' length 15033 bytes (14 KB)

==================================================

downloaded 14 KB


trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/biomaRt_2.58.2.tar.gz'

Content type 'application/x-gzip' length 670061 bytes (654 KB)

==================================================

downloaded 654 KB


trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/rtracklayer_1.62.0.tar.gz'

Content type 'application/x-gzip' length 4019225 bytes (3.8 MB)

==================================================

downloaded 3.8 MB


trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/GenomicFeatures_1.54.3.tar.gz'

Content type 'application/x-gzip' length 1180610 bytes (1.1 MB)

==================================================

downloaded 1.1 MB


trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/KEGGREST_1.42.0.tar.gz'

Content type 'application/x-gzip' length 22412 bytes (21 KB)

==================================================

downloaded 21 KB


trying URL 'https://bioconductor.org/packages/3.18/data/experiment/src/contrib/geneLenDataBase_1.38.0.tar.gz'

Content type 'application/x-gzip' length 100436531 bytes (95.8 MB)

==================================================

downloaded 95.8 MB


trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/AnnotationDbi_1.64.1.tar.gz'

Content type 'application/x-gzip' length 4359564 bytes (4.2 MB)

==================================================

downloaded 4.2 MB


trying URL 'https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GO.db_3.18.0.tar.gz'

Content type 'application/x-gzip' length 29013599 bytes (27.7 MB)

==================================================

downloaded 27.7 MB


trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/goseq_1.54.0.tar.gz'

Content type 'application/x-gzip' length 1769799 bytes (1.7 MB)

==================================================

downloaded 1.7 MB


* 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  


Emily Kunselman

unread,
Mar 8, 2024, 7:24:05 AMMar 8
to trinityrnaseq-users
Update: I was able to install all necessary R packages.

I am having an issue running analyze_diff_expr.pl because I receive the error: 

```

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


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