Error: object 'DEFAULT_CIRC_SEQS' is not exported by 'namespace:GenomicFeatures' #24

z626093820 · 2023-04-27T14:21:21Z

I installed R4.3 and got the following error in the manual installation of RiboseQC 1.1 , how to solve it, thank you very much！

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

polklin · 2023-04-28T07:42:36Z

Same error on my side, I'll keep you posted if I find a solution

z626093820 · 2023-04-28T07:43:59Z

Same error on my side, I'll keep you posted if I find a solution

THANK YOU!!!

polklin · 2023-04-28T07:55:41Z

GenomicFeatures removed this 'DEFAULT_CIRC_SEQS' global variable in version 1.40.0

See the NEWS file in https://github.com/Bioconductor/GenomicFeatures

    o Global constant DEFAULT_CIRC_SEQS (character vector) was removed. It is
      now defined in GenomeInfoDb but no longer exported, at least for now.

I'll try to install a previous verison (1.38) and see how it goes. But I need to find an archive for this package

polklin · 2023-04-28T08:59:24Z

Uninstall GenomicFeatures first and then reinstall it using:

devtools::install_github("Bioconductor/GenomicFeatures", ref="RELEASE_3_10")

polklin · 2023-04-28T09:47:47Z

By doing this i was able to import RiboseQC... but it did not work of course in the end ;)

I tried to reproduce the vignette example: https://htmlpreview.github.io/?https://github.com/lcalviell/Ribo-seQC/blob/master/RiboseQC.html

prepare_annotation_files(annotation_directory = ".",
                         twobit_file = "test_human.2bit",
                         gtf_file = "test_human.gtf",scientific_name = "Human.test",
                         annotation_name = "genc25_22M",export_bed_tables_TxDb = F,forge_BSgenome = T,create_TxDb = T)

I got the following error:

Creating the BSgenome package ... Fri Apr 28 11:41:25 2023
Creating package in /home/paul/projects/RiboseQC-test/out/BSgenome.Human.test.genc2522M 
Copying '/home/paul/projects/RiboseQC-test/test_human.2bit' to '/home/paul/projects/RiboseQC-test/out/BSgenome.Human.test.genc2522M/inst/extdata/single_sequences.2bit' ... DONE
Creating the BSgenome package --- Done! Fri Apr 28 11:41:26 2023
Installing the BSgenome package ... Fri Apr 28 11:41:26 2023
── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/home/paul/projects/RiboseQC-test/out/BSgenome.Human.test.genc2522M/DESCRIPTION’ ...
─  preparing ‘BSgenome.Human.test.genc2522M’:
✔  checking DESCRIPTION meta-information
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘BSgenome.Human.test.genc2522M_1.0.tar.gz’
   
Running /usr/lib/R/bin/R CMD INSTALL /tmp/RtmpWIB0sS/BSgenome.Human.test.genc2522M_1.0.tar.gz --install-tests 
* installing to library ‘/home/paul/R/x86_64-pc-linux-gnu-library/4.2’
* installing *source* package ‘BSgenome.Human.test.genc2522M’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BSgenome.Human.test.genc2522M)
Installing the BSgenome package --- Done! Fri Apr 28 11:41:49 2023
Creating the TxDb object ... Fri Apr 28 11:41:49 2023
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Creating the TxDb object --- Done! Fri Apr 28 11:41:51 2023
Extracting genomic regions ... Fri Apr 28 11:41:51 2023
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'reduce': error in evaluating the argument 'x' in selecting a method for function 'setdiff': object 'fancy_mseq' not found
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.

The error message object 'fancy_mseq' not found comes from the S4Vectors library.
It does make sense of course since the function has been removed: Bioconductor/S4Vectors@07a75c7

I thus tried to uninstall my recent S4Vectors and install a former one but none builds...

I think without clear explanations on what are the requirements and their corresponding versions, it will be very difficult to make RiboseQC work now, since the library is not maintained at all

z626093820 · 2023-04-29T04:31:47Z

By doing this i was able to import RiboseQC... but it did not work of course in the end ;)

I tried to reproduce the vignette example: https://htmlpreview.github.io/?https://github.com/lcalviell/Ribo-seQC/blob/master/RiboseQC.html

prepare_annotation_files(annotation_directory = ".",
                         twobit_file = "test_human.2bit",
                         gtf_file = "test_human.gtf",scientific_name = "Human.test",
                         annotation_name = "genc25_22M",export_bed_tables_TxDb = F,forge_BSgenome = T,create_TxDb = T)

I got the following error:

Creating the BSgenome package ... Fri Apr 28 11:41:25 2023
Creating package in /home/paul/projects/RiboseQC-test/out/BSgenome.Human.test.genc2522M 
Copying '/home/paul/projects/RiboseQC-test/test_human.2bit' to '/home/paul/projects/RiboseQC-test/out/BSgenome.Human.test.genc2522M/inst/extdata/single_sequences.2bit' ... DONE
Creating the BSgenome package --- Done! Fri Apr 28 11:41:26 2023
Installing the BSgenome package ... Fri Apr 28 11:41:26 2023
── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/home/paul/projects/RiboseQC-test/out/BSgenome.Human.test.genc2522M/DESCRIPTION’ ...
─  preparing ‘BSgenome.Human.test.genc2522M’:
✔  checking DESCRIPTION meta-information
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘BSgenome.Human.test.genc2522M_1.0.tar.gz’
   
Running /usr/lib/R/bin/R CMD INSTALL /tmp/RtmpWIB0sS/BSgenome.Human.test.genc2522M_1.0.tar.gz --install-tests 
* installing to library ‘/home/paul/R/x86_64-pc-linux-gnu-library/4.2’
* installing *source* package ‘BSgenome.Human.test.genc2522M’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BSgenome.Human.test.genc2522M)
Installing the BSgenome package --- Done! Fri Apr 28 11:41:49 2023
Creating the TxDb object ... Fri Apr 28 11:41:49 2023
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Creating the TxDb object --- Done! Fri Apr 28 11:41:51 2023
Extracting genomic regions ... Fri Apr 28 11:41:51 2023
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'reduce': error in evaluating the argument 'x' in selecting a method for function 'setdiff': object 'fancy_mseq' not found
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.

The error message object 'fancy_mseq' not found comes from the S4Vectors library. It does make sense of course since the function has been removed: Bioconductor/S4Vectors@07a75c7

I thus tried to uninstall my recent S4Vectors and install a former one but none builds...

I think without clear explanations on what are the requirements and their corresponding versions, it will be very difficult to make RiboseQC work now, since the library is not maintained at all

I slove this by install other vision, you can try:

library("devtools")
install_github("hsinyenwu/RiboseQC_R4.2.1")
library("RiboseQC")

polklin · 2023-05-09T15:11:37Z

Thanks for the suggestion @z626093820 !

Unfortunately, I still got the following error on my side:
error in evaluating the argument 'x' in selecting a method for function 'reduce': error in evaluating the argument 'x' in selecting a method for function 'setdiff': object 'fancy_mseq' not found

Leo-ccc · 2023-06-08T07:26:37Z

Hi polklin !
I ran into same problems, it worked after I updated R (R 4.1.3 to R4.3.0) and all dependences.

Here is my question and responses, you can give it a try.
Bioconductor/GenomicRanges#78 (comment)

Hope it can help you! Good luck!

polklin · 2023-06-08T07:50:02Z

Hello @Leo-ccc, thanks a lot for sharing this thread !

So if I summarize, you installed R-4.3.0, installed the latest version of Bioconductor (3.17), and then installed RiboseQC.
Which RiboseQC did you installed ? (hsinyenwu/RiboseQC_R4.2.1, or the one from the ohlerlab github repo ?)

Best regards

Leo-ccc · 2023-06-08T08:03:59Z

Yes, I installed hsinyenwu/RiboseQC_R4.2.1.

Another way is that downloading source file and delete importFrom(GenomicFeatures,DEFAULT_CIRC_SEQS) in NAMESPACE
. It might be a little complicated.

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Error: object 'DEFAULT_CIRC_SEQS' is not exported by 'namespace:GenomicFeatures' #24

Error: object 'DEFAULT_CIRC_SEQS' is not exported by 'namespace:GenomicFeatures' #24

z626093820 commented Apr 27, 2023

polklin commented Apr 28, 2023

z626093820 commented Apr 28, 2023

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z626093820 commented Apr 29, 2023

polklin commented May 9, 2023

Leo-ccc commented Jun 8, 2023

polklin commented Jun 8, 2023

Leo-ccc commented Jun 8, 2023

Error: object 'DEFAULT_CIRC_SEQS' is not exported by 'namespace:GenomicFeatures' #24

Error: object 'DEFAULT_CIRC_SEQS' is not exported by 'namespace:GenomicFeatures' #24

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z626093820 commented Apr 27, 2023

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