BiocGenerics built with R 3.4.2 changes behaviour
2
4
Entering edit mode
ginggs ▴ 40
@ginggs-14076
Last seen 7.1 years ago

Building BiocGenerics with the admittedly very new R 3.4.2 causes failures in unit tests of at least IRanges and VariantAnnotation.

IRanges RUnit Tests - 91 test functions, 2 errors, 0 failures
ERROR in test_AtomicList_general: Error in match.arg(method) : 'arg' must be of length 1
ERROR in test_AtomicList_numerical: Error in match.arg(method) : 'arg' must be of length 1

VariantAnnotation RUnit Tests - 80 test functions, 1 error, 0 failures
ERROR in test_VRanges_vcf: Error in match.arg(method) : 'arg' must be of length 1

Any suggestions on how to troubleshoot this further?

 

biocgenerics iranges variantannotation • 2.3k views
ADD COMMENT
2
Entering edit mode

Hi,

After installing R 3.4.2 I was able to reproduce this. The upgrade to R 3.4.2 also caused many other failures in many other Bioconductor packages. We advice users to NOT upgrade their installation to R 3.4.2 while we investigate this.

Cheers,

H.

ADD REPLY
0
Entering edit mode

Thanks for confirming!  Sorry, I didn't see your reply until I had already sent the follow up comment.

ADD REPLY
1
Entering edit mode
@herve-pages-1542
Last seen 13 hours ago
Seattle, WA, United States

There is a regression in R 3.4.2 that affects S4 generics with dispatch on the ellipsis. The bug is in the methods package and breaks code like sapply(x, paste, collapse="") (where x is a list of character vectors) by not passing the collapse argument to the internal calls to paste(). We've implemented a workaround in BiocGenerics that should fix generic functions paste, ordercbindrbindmapply, pmaxpminpmax.int, and pmin.int.

The fix is in BiocGenerics 0.22.1 (release) and 0.23.3 (devel). Both versions should become available via biocLite() in the next 12-15 hours.

Cheers,

H.

ADD COMMENT
0
Entering edit mode
ginggs ▴ 40
@ginggs-14076
Last seen 7.1 years ago

This is already partially fixed in git, S4Vectors:

  •     Work around regression in R 3.4.2 that breaks "order" (and indirectly "sort") method for List objects.
  •     More work around regression in R 3.4.2 that breaks "order" (and indirectly "sort") method for List objects.

and IRanges:

  • Fix default value for 'method' argument in "order" method for Ranges objects (must be the same as in base::order()).

 

 

ADD COMMENT

Login before adding your answer.

Traffic: 533 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6