Error in prepare_annotation_files with latetst version of R #21

sgraindorge · 2022-05-17T09:44:00Z

Hi !

I got this message while running the prepare_annotation_files command.
Could you tell me what I should change to make it work ?
Thanks

Stefanie

Creating the TxDb object --- Done! Tue May 17 11:36:29 2022
Extracting genomic regions ... Tue May 17 11:36:29 2022
Erreur : disjointExons() is defunct in BioC 3.15. Please use exonicParts() instead.
De plus : Messages d'avis :
1: Dans forgeBSgenomeDataPkg(y, seqs_srcdir = seqs_srcdir, destdir = destdir,  :
  field 'provider_version' is deprecated in favor of 'genome'
2: Dans forgeBSgenomeDataPkg(y, seqs_srcdir = seqs_srcdir, destdir = destdir,  :
  field 'release_name' is deprecated

The text was updated successfully, but these errors were encountered:

bribibel · 2022-08-06T11:54:06Z

I am getting the same error message (in English). Thanks in advance

Tim-Yu · 2022-09-08T12:37:35Z

Hi,

I faced a similar error in another package they wrote, it seems that Bioc updated some packages and changed some functions (disjointExons). I fixed the package I was using and I think my quick fix may also work here (by replacing disjointExons with exonicParts and changing the format back). You may want to try installing my modified version via Tim-Yu/RiboseQC?

install_github(repo = "Tim-Yu/RiboseQC")

BW,
Tim

bribibel · 2022-09-09T15:06:54Z

Thanks! I will have to try that out. Best of luck with your experiments!

hsinyenwu · 2022-09-14T16:27:16Z

It seems that modified RiboseQC does not work for me (but thanks Tim for trying!). The output was bigger than before. It seems that the BS genome object was not created properly using Arabidopsis genome and annotation and cannot be used for RiboseQC_analysis (see below for error message). RiboseQC ran okay with R4.1.3. Hopefully it got fixed soon.

#The Araport11_20220629.gtf_Rannot was created by the updated RiboseQC.
RiboseQC_analysis(annotation_file="~/Desktop/Araport11_20220629.gtf_Rannot",bam_files = "~/Desktop/star_2016_ribo_R1Aligned.chr1_1to10M.bam",report_file = "Root1_test.html",write_tmp_files = F)

Loading annotation files in ~/Desktop/Araport11_20220629.gtf_Rannot ... Wed Sep 14 12:58:39 2022
Error in get(library(GTF_annotation$genome, character.only = TRUE)) : 
  first argument has length > 1

hsinyenwu · 2022-09-15T01:39:46Z

Okay it worked after using Tim's modification and also removed this line genome_sequence<-get(library(GTF_annotation$genome,character.only = TRUE)) from the load_annotation function. Thanks Tim!

sgraindorge · 2022-09-20T09:19:23Z

Hi everybody.
I downloaded Tim's version this morning. No genome_sequence in the code ...
So I run it as is and get this new error message :

prepare_annotation_files(annotation_directory, twobit_file, gtf_file,
+                          scientific_name = "Arabidopsis.thaliana", annotation_name = "TAIR10.1",
+                          export_bed_tables_TxDb = T, forge_BSgenome = T, create_TxDb = T)
Creating the BSgenome package ... Tue Sep 20 11:07:47 2022
Error in download.file(url, destfile, quiet = TRUE) : 
  cannot open URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/735/GCF_000001735.4_TAIR10.1/GCF_000001735.4_TAIR10.1_assembly_report.txt'
In addition: Warning messages:
1: In forgeBSgenomeDataPkg(y, seqs_srcdir = seqs_srcdir, destdir = destdir,  :
  field 'provider_version' is deprecated in favor of 'genome'
2: In forgeBSgenomeDataPkg(y, seqs_srcdir = seqs_srcdir, destdir = destdir,  :
  field 'release_name' is deprecated`

I don't know why it is trying to download stuff knowing I give him the files he needs...
If you have any idea I would be very grateful
Thanks

Tim-Yu · 2022-09-20T14:23:49Z

Hi everybody. I downloaded Tim's version this morning. No genome_sequence in the code ... So I run it as is and get this new error message :

prepare_annotation_files(annotation_directory, twobit_file, gtf_file,
+                          scientific_name = "Arabidopsis.thaliana", annotation_name = "TAIR10.1",
+                          export_bed_tables_TxDb = T, forge_BSgenome = T, create_TxDb = T)
Creating the BSgenome package ... Tue Sep 20 11:07:47 2022
Error in download.file(url, destfile, quiet = TRUE) : 
  cannot open URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/735/GCF_000001735.4_TAIR10.1/GCF_000001735.4_TAIR10.1_assembly_report.txt'
In addition: Warning messages:
1: In forgeBSgenomeDataPkg(y, seqs_srcdir = seqs_srcdir, destdir = destdir,  :
  field 'provider_version' is deprecated in favor of 'genome'
2: In forgeBSgenomeDataPkg(y, seqs_srcdir = seqs_srcdir, destdir = destdir,  :
  field 'release_name' is deprecated`

I don't know why it is trying to download stuff knowing I give him the files he needs... If you have any idea I would be very grateful Thanks

Hi, I am confused with the error above. This should be an offline function I think? The warnings were fine.

sgraindorge · 2022-09-23T08:37:31Z

Hi !

I found that by just removing the =NULL from the first line : prepare_annotation_files(annotation_directory, twobit_file = NULL, gtf_file,... it didn't try to download files on internet anymore.

see ohlerlab#21 (comment); fixed by commenting out the line that causes the error

mahabubp · 2022-10-19T09:18:50Z

Hi everyone,

I installed Tim-Yu's version of RiboseQC today and I got the following error while preparing the annotation files. Could someone please look into this error and help me generate the annotation files. Thanks.

Error in prepare_annotation_files("~/annotation", "/home/lrge/Homo_sapiens.2bit", :
length(unique(gtfdata$transcript_id)) == n_transcripts is not TRUE
In addition: Warning messages:
1: In forgeBSgenomeDataPkg(y, seqs_srcdir = seqs_srcdir, destdir = destdir, :
field 'provider_version' is deprecated in favor of 'genome'
2: In forgeBSgenomeDataPkg(y, seqs_srcdir = seqs_srcdir, destdir = destdir, :
field 'release_name' is deprecated
3: In .get_cds_IDX(mcols0$type, mcols0$phase) :
The "phase" metadata column contains non-NA values for features of type stop_codon. This information was ignored.

Tyuewww · 2023-04-07T07:46:46Z

Hi everyone,

I installed Tim-Yu's version of RiboseQC today and I got the following error while preparing the annotation files. Could someone please look into this error and help me generate the annotation files. Thanks.

Error in prepare_annotation_files("~/annotation", "/home/lrge/Homo_sapiens.2bit", : length(unique(gtfdata$transcript_id)) == n_transcripts is not TRUE In addition: Warning messages: 1: In forgeBSgenomeDataPkg(y, seqs_srcdir = seqs_srcdir, destdir = destdir, : field 'provider_version' is deprecated in favor of 'genome' 2: In forgeBSgenomeDataPkg(y, seqs_srcdir = seqs_srcdir, destdir = destdir, : field 'release_name' is deprecated 3: In .get_cds_IDX(mcols0$type, mcols0$phase) : The "phase" metadata column contains non-NA values for features of type stop_codon. This information was ignored.

Hi !
I just ran into the same problem. Have you solved it? Could you give me some advice please?
Thank you very much！

mahabubp · 2023-04-14T13:23:27Z

Hi, sorry for the super delayed response. If you haven't solved this issue, here is the solution.

I downloaded the latest version (RiboseQC_1.1.tar.gz ) from here https://github.com/ohlerlab/RiboseQC/releases. I just removed the line 2283 (genome_sequence<-get(library(GTF_annotation$genome,character.only = TRUE)) from the load_annotation function in the riboseqc.R file in R folder and installed the package locally. Magically it worked. Give it a try. Hope it works for you too. Good luck.

Tyuewww · 2023-04-21T00:59:44Z

Thank you very much for your reply, it helped me a lot！

…

---- Replied Message ---- | From | Mahabub ***@***.***> | | Date | 04/14/2023 21:23 | | To | ***@***.***> | | Cc | ***@***.***>***@***.***> | | Subject | Re: [ohlerlab/RiboseQC] Error in prepare_annotation_files with latetst version of R (Issue #21) | Hi, sorry for the super delayed response. If you haven't solved this issue, here is the solution. I downloaded the latest version (RiboseQC_1.1.tar.gz ) from here https://github.com/ohlerlab/RiboseQC/releases. I just removed the line 2283 (genome_sequence<-get(library(GTF_annotation$genome,character.only = TRUE)) from the load_annotation function in the riboseqc.R file in R folder and installed the package locally. Magically it worked. Give it a try. Hope it works for you too. Good luck. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***>

polklin · 2023-04-24T11:01:06Z

Hi @mahabubp,

thank you very much for the suggestion !
I am not very familiar with R, could you elaborate a bit more the installation process ?
Do I need to install dependencies beforehand in order to make the installation work ?

I downloaded the "RiboseQC_1.1.tar.gz" you mentioned, and commented the line 2283.
I then create a new tar.gz file after this modification.

Trying

install.packages("/data/users/pklein/projects/riboseQC/RiboseQC.tar.gz", repos = NULL, type="source")

gives me a:

ERROR: cannot extract package from ‘/data/users/pklein/projects/riboseQC/RiboseQC.tar.gz’

Cheers

mahabubp · 2023-04-25T07:44:44Z

Hi, I installed it directly on R studio. In R studio click on Tools -> install packages -> install from Package Archive File (tar.gz). Package archive: select the Archive file from your folder and install it. If any dependencies are missing please try to install them before you could install RiboseQC. Hope this information helps you. Good luck.

polklin · 2023-04-27T12:21:24Z

thanks @mahabubp

z626093820 · 2023-04-27T12:45:03Z

Hi, I installed it directly on R studio. In R studio click on Tools -> install packages -> install from Package Archive File (tar.gz). Package archive: select the Archive file from your folder and install it. If any dependencies are missing please try to install them before you could install RiboseQC. Hope this information helps you. Good luck.

hello, i have error in install RiboseQC, What is your R version? THANK YOU！

mahabubp · 2023-04-27T13:07:47Z

Its R 4.3.0. May be you have an old version of R. Try to update it first then install RiboseQC.

z626093820 · 2023-04-27T13:21:54Z

Its R 4.3.0. May be you have an old version of R. Try to update it first then install RiboseQC.

I reinstalled R4.3 and got the following error in the manual installation of RiboseQC, did you encounter it and how to solve it, thank you very much！

Error: object 'DEFAULT_CIRC_SEQS' is not exported by 'namespace:GenomicFeatures'
Execution halted

mahabubp · 2023-04-27T14:16:30Z

No, I didn't face this issue during installation. I have no clue what this issue about even. May be try to install the package from github and see if it works. If not please contact the admin of this package. Good luck.

polklin · 2023-04-28T09:51:22Z

Sorry to disturb again @mahabubp, may I ask the libraries version you have please ?
Especially the dependencies versions when you load RiboseQC ?

That would help a lot !
Best,
Paul

mahabubp · 2023-04-28T15:40:11Z

Hi @z626093820,
I updated my RStudio (4.3.0) recently and I totally forgot to install RiboseQC on it before. But today I did install the package with no issues. I think you forgot to install devtools (install.packages("devtools")) on your new RStudio. Please do that first before you can install RiboseQC package (install.packages("~/RiboseQC", repos = NULL, type = "source")). Good luck.

mahabubp · 2023-04-28T15:50:10Z

Hi Paul (@polklin),

Here is the session info of my RiboseQC run. FYI: I installed the Bioconductor package 3.17 on my RStudio.

sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=cs_CZ.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=cs_CZ.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=cs_CZ.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=cs_CZ.UTF-8 LC_IDENTIFICATION=C

time zone: Europe/Prague
tzcode source: system (glibc)

attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base

other attached packages:
[1] BSgenome.Homo.sapiens.genc25_1.0 RiboseQC_0.99.0 jsonlite_1.8.4
[4] GenomicFeatures_1.52.0 AnnotationDbi_1.62.0 viridis_0.6.2
[7] viridisLite_0.4.1 ggpubr_0.6.0 gridExtra_2.3
[10] DT_0.27 knitr_1.42 ggplot2_3.4.2
[13] reshape2_1.4.4 GenomicFiles_1.36.0 BiocParallel_1.34.0
[16] BSgenome_1.68.0 GenomicAlignments_1.36.0 SummarizedExperiment_1.30.0
[19] Biobase_2.60.0 MatrixGenerics_1.12.0 matrixStats_0.63.0
[22] rtracklayer_1.60.0 rmarkdown_2.21 Rsamtools_2.16.0
[25] Biostrings_2.68.0 XVector_0.40.0 GenomicRanges_1.52.0
[28] GenomeInfoDb_1.36.0 IRanges_2.34.0 S4Vectors_0.38.0
[31] BiocGenerics_0.46.0 devtools_2.4.5 usethis_2.1.6

loaded via [1] RColorBrewer_1.1-3 [6] BiocIO_1.10.0 [11] rstatix_0.7.2 [16] sass_0.4.5 [21] cachem_1.0.7 [26] R6_2.5.1 [31] colorspace_2.1-0 [36] RSQLite_2.3.1 [41] abind_1.4-5 [46] backports_1.4.1 [51] ggsignif_0.6.4 [56] rjson_0.2.21 [61] callr_3.7.3 [66] tidyr_1.3.0 [71] pillar_1.9.0 [76] lattice_0.21-8 [81] stringi_1.7.12 [86] BiocManager_1.30.20 [91] processx_3.8.1 [96] parallel_4.3.0 [101] urlchecker_1.0.1 [106] crayon_1.5.2 a namespace (and not attached):
rstudioapi_0.14 magrittr_2.0.3 farver_2.1.1 fs_1.6.2
zlibbioc_1.46.0 vctrs_0.6.2 memoise_2.0.1 RCurl_1.98-1.12
htmltools_0.5.5 progress_1.2.2 curl_5.0.0 broom_1.0.4
bslib_0.4.2 desc_1.4.2 htmlwidgets_1.6.2 plyr_1.8.8
mime_0.12 lifecycle_1.0.3 pkgconfig_2.0.3 Matrix_1.5-4
fastmap_1.1.1 GenomeInfoDbData_1.2.10 shiny_1.7.4 digest_0.6.31
ps_1.7.5 rprojroot_2.0.3 pkgload_1.3.2 crosstalk_1.2.0
labeling_0.4.2 filelock_1.0.2 fansi_1.0.4 httr_1.4.5
compiler_4.3.0 remotes_2.4.2 bit64_4.0.5 withr_2.5.0
carData_3.0-5 DBI_1.1.3 highr_0.10 pkgbuild_1.4.0
biomaRt_2.56.0 rappdirs_0.3.3 DelayedArray_0.25.0 sessioninfo_1.2.2
tools_4.3.0 httpuv_1.6.9 glue_1.6.2 restfulr_0.0.15
promises_1.2.0.1 grid_4.3.0 generics_0.1.3 gtable_0.3.3
hms_1.1.3 xml2_1.3.4 car_3.1-2 utf8_1.2.3
stringr_1.5.0 later_1.3.0 dplyr_1.1.2 BiocFileCache_2.8.0
bit_4.0.5 tidyselect_1.2.0 miniUI_0.1.1.1 xfun_0.39
yaml_2.3.7 evaluate_0.20 codetools_0.2-19 tibble_3.2.1
cli_3.6.1 xtable_1.8-4 jquerylib_0.1.4 munsell_0.5.0
Rcpp_1.0.10 dbplyr_2.3.2 png_0.1-8 XML_3.99-0.14
ellipsis_0.3.2 blob_1.2.4 prettyunits_1.1.1 profvis_0.3.7
bitops_1.0-7 VariantAnnotation_1.46.0 scales_1.2.1 purrr_1.0.1
rlang_1.1.0 cowplot_1.1.1 KEGGREST_1.40.0

After running into this[1] issue, I saw a proposed solution of removing the offending line entirely. Looking at the code it seems like that should be fine to do — the current code does this: genome_sequence<-get(library(GTF_annotation$genome,character.only = TRUE)) library(GTF_annotation$genome,character.only = TRUE) genome_sequence<-get(GTF_annotation$genome) This fails because `library(…)` returns a vector of attached libraries, not just the single one loaded, which `get` can't deal with. `git blame` says this line has been there since 2019, and I'm not sure how this has ever worked. Maybe no one has ever gone through this branch of the enclosing `if` statement, or maybe R's `library` function changed at some point? I'm not sure, and I'm still a newbie at R so I don't know how to nail that down further. Returning to the code, the two lines following that problematic line just seem to do effectively the same thing, but in two steps instead of one (indentation mine): genome_sequence<-get(library(GTF_annotation$genome,character.only = TRUE)) library(GTF_annotation$genome,character.only = TRUE) genome_sequence<-get(GTF_annotation$genome) So I think it's safe to just remove this line entirely. [1] ohlerlab#21 (comment)

damhof added a commit to damhof/RiboseQC that referenced this issue Sep 29, 2022

fix loading annotation files

de23367

see ohlerlab#21 (comment); fixed by commenting out the line that causes the error

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Error in prepare_annotation_files with latetst version of R #21

Error in prepare_annotation_files with latetst version of R #21

sgraindorge commented May 17, 2022

bribibel commented Aug 6, 2022

Tim-Yu commented Sep 8, 2022

bribibel commented Sep 9, 2022

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hsinyenwu commented Sep 15, 2022

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Tyuewww commented Apr 21, 2023 via email

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z626093820 commented Apr 27, 2023

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mahabubp commented Apr 27, 2023

polklin commented Apr 28, 2023

mahabubp commented Apr 28, 2023

mahabubp commented Apr 28, 2023

Error in prepare_annotation_files with latetst version of R #21

Error in prepare_annotation_files with latetst version of R #21

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