forked from bioconda/bioconda-recipes
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathbuild-fail-blacklist
1108 lines (942 loc) · 26.8 KB
/
build-fail-blacklist
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
# Currently kills bulk, and dependants
recipes/bioconductor-missmethyl
recipes/bioconductor-conumee
recipes/r-shazam
recipes/r-scoper
recipes/r-dowser
recipes/bioconductor-chipxpressdata
recipes/bioconductor-chipxpress
recipes/bioconductor-meal
recipes/bioconductor-dmrcate
recipes/bioconductor-methylgsa
recipes/bioconductor-champ
recipes/bioconductor-appreci8r
recipes/bioconductor-mirsm
# Needs r-xgboost migration
recipes/bioconductor-bambu
recipes/bioconductor-bayesspace
recipes/bioconductor-ccmap
recipes/bioconductor-classifyr
recipes/bioconductor-gnet2
recipes/bioconductor-infinityflow
recipes/bioconductor-mistyr
recipes/bioconductor-scate
recipes/bioconductor-scdblfinder
recipes/bioconductor-scds
recipes/bioconductor-trena
recipes/bioconductor-flames
recipes/bioconductor-singlecelltk
# Allegedly requires ancient gatb
recipes/lordec
# Uses all the RAM/time on github actions
recipes/octopus
recipes/bttcmp
recipes/bttoxin_scanner
recipes/cgat-apps
recipes/hatchet
recipes/hail
recipes/monocle3-cli
recipes/phenix
recipes/mtsv
# Fills the disk on the CI
recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5
recipes/bioconductor-mafdb.gnomad.r2.1.grch38
recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch37
recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch38
# x86_64-conda-linux-gnu-cc: error: unrecognized command-line option '-R'
recipes/ncbi-util-legacy
# HDF5 compatibility, https://github.com/mateidavid/nanocall/issues/38
recipes/nanocall
# source code no longer available
recipes/bugseq-porechop
# move to conda-forge
recipes/autolog
recipes/avro-python2
recipes/cityhash
recipes/collectl
recipes/elasticluster
recipes/epydoc
recipes/esmre
recipes/forked-path
recipes/gnuplot-py
recipes/justbackoff
recipes/kid
recipes/myriad
recipes/nose-capturestderr
recipes/pdfkit
recipes/perl-mozilla-ca
recipes/perl-pcap
recipes/perl-getopt-argvfile
recipes/perl-data-dump
recipes/perl-text-csv_xs
recipes/perl-probe-perl
recipes/perl-lwp-protocol-https
recipes/perl-libwww-perl
recipes/perl-test-xml
recipes/perl-www-mechanize
recipes/perl-rest-client
recipes/perl-net-http
recipes/perl-lwp-simple
recipes/perl-soap-lite
recipes/perl-xml-twig
recipes/perl-digest-md5-file
recipes/perl-graphviz
recipes/perl-xml-dom-xpath
recipes/perl-xml-dom
recipes/perl-util-properties
recipes/pyasp
recipes/pyexcelerator
recipes/pyhashxx
recipes/pyopt
recipes/pysvg
recipes/pyx
recipes/rdfextras
recipes/scala
recipes/sharedmem
recipes/stacks_summary
recipes/tgt
recipes/workspace
recipes/wtforms-alchemy
recipes/wtforms-components
recipes/xmlbuilder
recipes/yaggo
# the following packages have open PRs labeled with "Move to conda-forge"
recipes/perl-alien-build
recipes/perl-alien-libxml2
recipes/perl-date-manip
recipes/perl-datetime-timezone
recipes/perl-devel-checklib
recipes/perl-ffi-checklib
recipes/perl-file-sharedir-install
recipes/perl-graphviz
recipes/perl-hpc-runner-command-plugin-logger-sqlite
recipes/perl-html-form
recipes/perl-http-message
recipes/perl-image-info
recipes/perl-ipc-run
recipes/perl-module-corelist
recipes/perl-parallel-iterator
recipes/perl-pdf-api2
recipes/perl-perlio-utf8_strict
recipes/perl-sereal-decoder
recipes/perl-sereal-encoder
recipes/perl-term-progressbar
recipes/perl-uri
recipes/perl-xml-libxml
recipes/scoop
recipes/wheezy.template
# perl package with no proper installation method
recipes/feelnc
# incompatible with htslib >1.10 https://github.com/statgen/popscle/issues/57
recipes/popscle
# Maven no longer accepts http connections https://github.com/rdpstaff/ReadSeq/issues/2
recipes/rdp-readseq
# Only specific versions are failing
recipes/emmix/1.3
recipes/hyphy/2.3.11
recipes/skewer/0.1.126
recipes/blast/2.2.31
recipes/bedtools/2.26.0
recipes/opsin/1.4.0
recipes/opsin/2.1.0
recipes/meme/4.11.1
recipes/meme/4.11.2
recipes/meme/4.8.1
recipes/bcftools-gtc2vcf-plugin/1.9
recipes/panx/1.6.0
recipes/panx/1.5.0
recipes/haploclique/1.3.1
recipes/blast/2.5.0
# Unclear that the following old version is still needed, but the main recipe has an older version?!?
recipes/mira/4.9.6
# need to fix the download location, the checksum changes everytime
recipes/osra/2.1.0
recipes/imfusion/0.3.2
# can't open file setup.py
recipes/meneco/1.5.2
# Permission denied ESTscan
recipes/perl-estscan2/2.1
# Source code no longer easily available
recipes/strip_it/1.0.2
recipes/shape_it/1.0.1
recipes/tqdist/1.0.0
recipes/ocrad/0.21
recipes/perl-estscan1/1.3
recipes/bwa/0.6.2
# reprocessed to here
# fails compilation in bulk on Linux
recipes/paragraph
recipes/selectsequencesfrommsa
recipes/rappas
recipes/centrifuge
recipes/nasp
recipes/mmvc
recipes/expansionhunter
recipes/gemma
recipes/roary
recipes/deltabs
recipes/gottcha
recipes/pepnovo
recipes/ea-utils
recipes/nextgenmap
recipes/extract_fullseq
recipes/igor_vdj
recipes/pargenes
recipes/porfast
recipes/agg
recipes/hg-color
recipes/bandage
recipes/prosolo
recipes/ratt
recipes/graphclust-wrappers
recipes/swga
recipes/jvarkit-bam2wig
recipes/jvarkit-bam2svg
recipes/jvarkit-msa2vcf
recipes/rxdock
recipes/cath-tools
recipes/phame
recipes/goetia
recipes/consel
recipes/isaac4
recipes/clame
recipes/prosic
recipes/dms
recipes/variant_tools
recipes/translig
recipes/lsc
recipes/rambo-k
recipes/mobster
recipes/visceral-evaluatesegmentation
recipes/chicagotools
recipes/skewer
recipes/trim_isoseq_polya
recipes/ra/ra-assembler
recipes/pureclip
recipes/hulk
recipes/bolt-lmm
recipes/bmfilter
recipes/unitig-counter
recipes/probcons
recipes/spydrpick
recipes/bctools
recipes/bayestyper
recipes/group_humann2_uniref_abundances_to_go
recipes/isonclust2
recipes/bmtool
recipes/sibelia
recipes/var-agg
recipes/wham
recipes/percolator
# Segfaults in bulk on Linux 24.3.2021
recipes/dbgraph
recipes/mira
# Source code moved
recipes/astalavista
recipes/kggseq
recipes/hts-nim-tools
recipes/oligoarrayaux
recipes/coral
recipes/ngsep
recipes/rnabridge-denovo
recipes/eval
recipes/minorseq
recipes/prosampler
recipes/methylextract
recipes/blasr
recipes/asn2gb
recipes/skesa
recipes/orfm
recipes/maaslin
recipes/seqmap
recipes/micropita
recipes/assemblytics
recipes/nemo
recipes/pblaa
recipes/translatorx
recipes/meme/4.11.1
recipes/meme/4.8.1
recipes/bax2bam
recipes/break-point-inspector
recipes/embl-api-validator
recipes/readseq
recipes/smcounter2
recipes/compalignp
recipes/reaper
recipes/genie
recipes/admixture
recipes/mace
recipes/riboseq-rust
# vendors bzip2, samtools, etc.
recipes/rvtests
# Source URL no longer exists
recipes/python-mailund-newick
recipes/piret
# Requires obsolete matplotlib versions incompatible with our gfortran pinnings
recipes/riboplot
# Requires libXext.so.6 in the container
recipes/samsifter
# C++ syntax error: ../../lib/srprism/query_acct.hpp:118:51: error: expected primary-expression before ')' token { return query_info_[qn].MaxErr< paired >(); }
recipes/srprism
# Mulled test never completes
recipes/comparative-annotation-toolkit
# compilation or other errors in bulk
recipes/transcomb
recipes/detonate
recipes/bmtagger
# Killing bulk
recipes/rsat-core
# Packages failing in bulk that haven't yet received more attention
recipes/ig-checkflowtypes
recipes/bufet
recipes/mapsplice
recipes/pasta
recipes/halla
recipes/qtip
recipes/tagger
recipes/compare-reads
recipes/strainest
recipes/methylpy
recipes/t_coffee
recipes/shannon_cpp
recipes/ecopy
recipes/qiimetomaaslin
recipes/groopm
recipes/biolite
recipes/pauda
recipes/hicbrowser
recipes/vqsr_cnn
recipes/bam-readcount
recipes/mqc
recipes/roprofile
recipes/chanjo
recipes/xxmotif
recipes/phylip
recipes/gqt
recipes/diamond_add_taxonomy
recipes/shapemapper
recipes/rnftools
recipes/embassy-phylip
recipes/triform2
recipes/lcfit
recipes/tadarida-c
recipes/w4mclstrpeakpics
# KeyError: '>=1.0.6'
# (apparently due to bzip2 constraint)
recipes/sgcocaller
recipes/sscocaller
# numba import fails with no exception
recipes/sparse-neighbors-search
# needs specific clusterprofiler and enrichplot versions that are not currently available
recipes/vsclust
# having issues compiling on macOS
recipes/circle-map-cpp
# make: common": No such file or directory
recipes/conduit-assembler
# configure: error: cannot find required auxiliary files: config.guess config.sub
recipes/metabat2
recipes/bcftools-snvphyl-plugin
# error: no matching package named `bird_tool_utils` found location searched: https://github.com/wwood/galah#8440eeb8 required by package `galah v0.3.1 (https://github.com/wwood/galah#8440eeb8)` ... which satisfies git dependency `galah` of package `lorikeet-genome v0.7.3
recipes/lorikeet-genome
# rnamoves.c:(.text.RNA2_move_noLP_bpshift+0x1f): undefined reference to `close_bp'
recipes/kinsimriboswitch
# Package seems to build fine, but then can't be found when uploading for some reason.
# the built package /home/runner/miniconda/envs/bioconda/conda-bld/noarch/ngscheckmate-1.0.0-py27r42hdfd78af_4.tar.bz2 cannot be found
recipes/ngscheckmate
# configure: error: R package gtools not found.
# (even though r-gtools is in host: and run:
recipes/footprint
# Requests python3, but is written for python2
recipes/ctat-mutations
# Seems to download maven and then have java issues
recipes/megagta
# Unknown issues
recipes/cmv
recipes/fwdpp
recipes/parafly
recipes/smashbenchmarking
recipes/saffrontree
recipes/slclust
# tracking master branch
recipes/frc
# CMake Error at build-common/cmake/VersionHelper.cmake:11 (list):
recipes/somatic-sniper
# can't find file to patch at input line 3
recipes/erds
# non-standard test
recipes/fermikit
# build-error
recipes/mimodd
# error: possibly undefined macro: AM_GNU_GETTEXT
recipes/xcftools
# See https://github.com/bioconda/bioconda-recipes/pull/9458
recipes/spingo
# CMake Error: The source directory "/opt/conda/conda-bld/sqlitebrowser_1529759350498/work" does not appear to contain CMakeLists.txt.
recipes/sqlitebrowser
# no test, website down
recipes/sprinkles
# link not founds
recipes/soapcoverage
# download error
recipes/soapaligner
# missing tarball
recipes/sloika
recipes/genometools
recipes/nanonet
recipes/knot
recipes/jali
recipes/intervalstats
# missing dep
recipes/oligotyping
recipes/oligotyping/2.0
# missing file
recipes/shiver
# missing binary
recipes/semeta
# Various C++ errors
recipes/rdock
# WARNING (talloc,lib/libpytalloc-util.so.2.1.9): did not find - or even know where to look for: /lib64/libm.so.6
recipes/talloc
# Skipped: vnl from /opt/recipe defines build/skip for this configuration ({'c_compiler': 'toolchain_c'}).
recipes/vnl
# something wrong with the test
recipes/remurna
# Test uses a program that makes incorrect assumptions about shebangs (you can't reliably use "#!/usr/bin/env program --arguments")
recipes/amos
# aclocal error, but also downloads mauve tarballs, but there is now a mauve pkgs, is it still needed?
recipes/libmuscle
# compilation error
recipes/lightning
# unable to access jarfile
recipes/effectivet3
# url broken
recipes/e-pcr
# linker error
recipes/discovar-denovo
# depends on perl-pcap
recipes/brass
# oh no TPP is failing, it was a nightmare to get it to compile in the first place :(
recipes/tpp
# perl dependency estmapper not available for 5.26
recipes/wgs-assembler
# requires wgs-assembler, which has a build fail
recipes/sprai
# missing dependency
recipes/genomebaser
recipes/garnet
recipes/tablet
# RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml url=https://pypi.org/simple/funcsigs/
recipes/pytest-marks
recipes/hubward
recipes/phylotoast
# git checkout problem
recipes/icqsol
recipes/pout2mzid
# checksum always fails
recipes/ms
# sed: can't read /opt/conda/conda-bld/idba_1530055808563/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/bin/aclocal: No such file or directory
recipes/idba
# PREFIX/lib is a directory
recipes/proot
# bin/g++: Command not found
recipes/metavelvet-sl
recipes/metavelvet
# cp: target `/opt/conda/conda-bld/meryl_1530057980094/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/' is not a directory
recipes/metavelvet-sl-pipeline
# Conflicting numpy and qiime
recipes/koeken
# cp: cannot stat `./mapsembler2_extremities/build/mapsembler2_extremities': No such file or directory
recipes/mapsembler2
# Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!
recipes/primerprospector
# missing URL
recipes/intemap
# zlib missing
recipes/polymutt
# /opt/rh/devtoolset-2/root/usr/libexec/gcc/x86_64-redhat-linux/4.8.2/ld: cannot find -lc
recipes/piler
# /usr/bin/env: python -Es: No such file or directory
recipes/pizzly
# natsort conflicts with python
recipes/qcumber
# Tests failed for spanki-0.5.1-py27h24bf2e0_1.tar.bz2 - moving package to /opt/conda/conda-bld/broken
recipes/spanki
# broken pipe
recipes/antarna
# hashFunction.c:94: Error: invalid instruction suffix for `push'
recipes/soapdenovo2
# tarball missing and should be migrated I guess
recipes/ngseqbasic
# missing bioc package
recipes/customprodb
# Error: Could not find or load main class edu.duke.igsp.gkde.Main
recipes/fseq
# node error
recipes/azure-cli
recipes/arvados-cli
# takes to long to install
recipes/bcbio-rnaseq
# missing python requirements?
recipes/illuminate
# dotnet not found
recipes/canvas
# perl script could not be found
recipes/rnaclust
# Unknown issues
recipes/lorma
recipes/microbecensus
recipes/minialign
recipes/nspdk
recipes/dreamtools
recipes/biomaj
recipes/cas-offinder
recipes/odose
# /opt/conda/conda-bld/pash_1531691261758/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/ruby/2.4.0/rubygems/core_ext/kernel_require.rb:55:in `require': cannot load such file -- brl/util/textFileUtil (LoadError)
recipes/pash
# Uses deprecated POSIX::tmpnam() function, not maintained, partially replaced by estscan 3.0
recipes/perl-btlib/0.19
# takes a long time and then fails?
recipes/kmerinshort
# chmod: cannot access `genblast_v1.0.4': No such file or directory
recipes/genblasta
# ImportError: cannot import name 'aveQual'
recipes/nanosplit
# Cpp no such file or dir
recipes/genepop
# Error: Unable to access jarfile
recipes/gfinisher
# gsl missing but specified
recipes/gfold
# compilation error, missing boost header
recipes/k-slam
# missing fortran lib, will fix this upstream
recipes/ig-checkfcs
# np-likeness scorer no such file or directory
recipes/np-likeness-scorer
# Throws an error during testing
recipes/reago
# Error during mulled testing on circleci
recipes/ra-integrate
# /boost/intrusive/list.hpp:123:22: error: ‘const bool boost::intrusive::list_impl<boost::intrusive::bhtraits<dng::pileup::Node, boost::intrusive::list_node_traits<void*>, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 1u>, long unsigned int, true, void>::safemode_or_autounlink’ is private
recipes/denovogear
# /opt/rh/devtoolset-2/root/usr/libexec/gcc/x86_64-redhat-linux/4.8.2/ld: cannot find -lboost_system
recipes/metaprob
# Fails testing
recipes/cap-mirseq
recipes/graphprot
# OSX related errors, Linux should be fine. Most of the non-perl issues are due to LLVM used as a compiler, GCC should be fine
recipes/cgat-scripts
recipes/smalt
recipes/oases
recipes/metavelvet-sl-feature-extraction
recipes/music
recipes/kraken-ea
recipes/gnu-getopt
recipes/domclust
recipes/flock
recipes/cmfinder
recipes/cortex_con
recipes/cosi2
recipes/cufflinks
recipes/esimsa
recipes/fastuniq
recipes/fgap
recipes/funcannot
recipes/genepender
recipes/ghostx
recipes/ls-gkm
recipes/mosaik
recipes/mustang
recipes/ngmerge
recipes/nlstradamus
recipes/panoct
recipes/pygresql
recipes/real
recipes/rmap
recipes/rnabob
recipes/sam
recipes/sff2fastq
recipes/snpomatic
recipes/soapdenovo2-gapcloser
recipes/spectral_hk
recipes/swiftlink
recipes/tedna
recipes/transtermhp
recipes/carna
# stringify can't find libmysqlclient.18
recipes/ucsc-overlapselect
recipes/ucsc-pslmap
# Source seems to have moved
recipes/discovar
# source code no longer available at URL
recipes/wade
# Requirements pinned down so much that rebuilds are prevented. (Some old deps may only be available on the old pks/free defaults channel.)
recipes/oncotator
# Depends on rdfextras with depends old pyparsing not available on conda-forge and pkgs/main (only on pkgs/free)
recipes/pacbio_falcon
# Depends on old matplotlib <1.5.0 not available on conda-forge and pkgs/main (only on pkgs/free)
recipes/pymix
# Depends on pymix, see above
recipes/ale
# Pinned to biopython=1.65 which is only availble through pkgs/free. If it doesn't break the package, the requirement should be set to biopython=1.70 or higher.
recipes/breakseq2
# R package build segfaults: [2020-07-28 05:38:00] Plotting genome...\n\n*** caught segfault ***\naddress (nil), cause 'memory not mapped'\n\nTraceback:\n 1: cairoVersion()\n 2: grSoftVersion()\n 3: symbolType1support()\n 4: optionSymbolFont(d$symbolfamily)\n 5: png(paste0(xargs$out, ".cnv.png"), units = "px", width = 1600, height = 1600, res = 300)
recipes/cnv_facets
# Depends on r-base and mentalist. The latter has has pinned down dependencies preventing the installation alongside other packages like r-base. Need to fix mentalist!
recipes/pathogist
# Uses binary wheel that have been deleted upstream (and are not available from depot.galaxyproject.org). To fix it, build from source
recipes/python-consensuscore2
# Pinned to older Bioconductor package version that is not build for current R
recipes/scater-scripts
recipes/sc3-scripts
# Warning: replacing previous import ‘BiocGenerics::combine’ by ‘gridExtra::combine’ when loading ‘RiboseQC’\nWarning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘RiboseQC’\nERROR: lazy loading failed for package ‘RiboseQC’\n* removing ‘$PREFIX/lib/R/library/RiboseQC’\nError: object ‘DEFAULT_CIRC_SEQS’ is not exported by 'namespace:GenomicFeatures'
recipes/riboseqc
# Some UnsatisfiableError
recipes/maaslin2
recipes/music-deconvolution
# Bulk times out while solving environment
recipes/mercat
recipes/panpasco
# Needs a bunch of fixes (remove outdated conda-forge::perl workaround, not symlinking compiler/linker, linker fixes, etc.).
recipes/arb-bio
# Source needs patching ("degree()" definition is ambiguous):
# BWTIL/data_structures/../common/../extern/bitvector/include/internal/bitvector.hpp:815:43: error: expression cannot be used as a function
# t.ranks(child, degree()) -= 1;
recipes/erne
# Vendors gsl but fails to compile it.
recipes/rseg
# Uses pyinstaller (why??) but doesn't run: "Cannot open self $PREFIX/bin/taco_run or archive $PREFIX/bin/taco_run.pkg"
recipes/taco
# Unknown issues
recipes/cnvetti
recipes/proteowizard
recipes/bibliospec
# OCaml/opam build fails
recipes/phylocsf
# Ruby build failes
recipes/protk
# Does not link include -lGL -lGLU when linking, might require libOSMesa.
recipes/connectome-workbench
# GSL linking problem (-lgsl not used?): "undefined reference to `gsl_ran_multinomial_pdf'"
recipes/merfishtools
# Build fails during boostrap of vendored Boost.
recipes/gvcftools
recipes/seer
# Can't compile
recipes/gplas
# compilation error and dependants
recipes/mmult
recipes/bioconductor-hilbertvisgui
recipes/bioconductor-travel
recipes/bioconductor-netboost
# some missing perl dependency
recipes/perl-biox-workflow-command
# python 2-only with C requiring graphiv. No longer supportable
recipes/sshmm
# Source code no longer easily available
recipes/cap3
recipes/bumbershoot
recipes/gerp
recipes/turbocor
# tool renamed
recipes/titan-gc
# failing in bulk for now
recipes/cmip
recipes/cesm
recipes/minnow
recipes/quip
recipes/conterminator
recipes/groot
recipes/mantis
recipes/apoc
recipes/quorum
recipes/curves
recipes/noresm
recipes/xsd
recipes/callstate
recipes/hypo
recipes/pb-falcon-phase
recipes/hiline
recipes/eqtlbma
recipes/selene-sdk
recipes/barriers
# Requires rmblast update
recipes/maker
# Takes hours to solve the environment
recipes/rop
# Need to redo the skeletons for these
recipes/ucsc-addcols
recipes/ucsc-ameme
recipes/ucsc-autodtd
recipes/ucsc-autosql
recipes/ucsc-autoxml
recipes/ucsc-avecols
recipes/ucsc-axtchain
recipes/ucsc-axtsort
recipes/ucsc-axtswap
recipes/ucsc-axttomaf
recipes/ucsc-axttopsl
recipes/ucsc-bamtopsl
recipes/ucsc-bedclip
recipes/ucsc-bedcommonregions
recipes/ucsc-bedcoverage
recipes/ucsc-bedextendranges
recipes/ucsc-bedgeneparts
recipes/ucsc-bedgraphpack
recipes/ucsc-bedintersect
recipes/ucsc-beditemoverlapcount
recipes/ucsc-bedjointaboffset
recipes/ucsc-bedpileups
recipes/ucsc-bedremoveoverlap
recipes/ucsc-bedrestricttopositions
recipes/ucsc-bedsort
recipes/ucsc-bedtogenepred
recipes/ucsc-bedtopsl
recipes/ucsc-bedweedoverlapping
recipes/ucsc-bigbedinfo
recipes/ucsc-bigbednameditems
recipes/ucsc-bigbedsummary
recipes/ucsc-bigbedtobed
recipes/ucsc-bigmaftomaf
recipes/ucsc-bigpsltopsl
recipes/ucsc-bigwigaverageoverbed
recipes/ucsc-bigwigcat
recipes/ucsc-bigwigcluster
recipes/ucsc-bigwigcorrelate
recipes/ucsc-bigwiginfo
recipes/ucsc-bigwigmerge
recipes/ucsc-blasttopsl
recipes/ucsc-catdir
recipes/ucsc-catuncomment
recipes/ucsc-chainantirepeat
recipes/ucsc-chainbridge
recipes/ucsc-chainfilter
recipes/ucsc-chainmergesort
recipes/ucsc-chainnet
recipes/ucsc-chainprenet
recipes/ucsc-chainsort
recipes/ucsc-chainsplit
recipes/ucsc-chainstitchid
recipes/ucsc-chainswap
recipes/ucsc-chaintoaxt
recipes/ucsc-chaintopsl
recipes/ucsc-chaintopslbasic
recipes/ucsc-checkagpandfa
recipes/ucsc-checkcoveragegaps
recipes/ucsc-checkhgfindspec
recipes/ucsc-checktablecoords
recipes/ucsc-chopfalines
recipes/ucsc-chromgraphfrombin
recipes/ucsc-chromgraphtobin
recipes/ucsc-clustergenes
recipes/ucsc-coltransform
recipes/ucsc-countchars
recipes/ucsc-crtreeindexbed
recipes/ucsc-crtreesearchbed
recipes/ucsc-dbsnoop
recipes/ucsc-dbtrash
recipes/ucsc-endsinlf
recipes/ucsc-estorient
recipes/ucsc-expmatrixtobarchartbed
recipes/ucsc-faalign
recipes/ucsc-facmp
recipes/ucsc-facount
recipes/ucsc-fafilter
recipes/ucsc-fafiltern
recipes/ucsc-fafrag
recipes/ucsc-fanoise
recipes/ucsc-faonerecord
recipes/ucsc-fapolyasizes
recipes/ucsc-farandomize
recipes/ucsc-farc
recipes/ucsc-fasize
recipes/ucsc-fasomerecords
recipes/ucsc-fasplit
recipes/ucsc-fastqstatsandsubsample
recipes/ucsc-fastqtofa
recipes/ucsc-fatofastq
recipes/ucsc-fatotab
recipes/ucsc-fatrans
recipes/ucsc-featurebits
recipes/ucsc-fetchchromsizes
recipes/ucsc-findmotif
recipes/ucsc-gaptolift
recipes/ucsc-genepredfilter
recipes/ucsc-genepredhisto
recipes/ucsc-genepredsinglecover
recipes/ucsc-genepredtofakepsl
recipes/ucsc-genepredtogtf
recipes/ucsc-genepredtomafframes
recipes/ucsc-genepredtoprot
recipes/ucsc-gensub2
recipes/ucsc-getrna
recipes/ucsc-getrnapred
recipes/ucsc-gff3topsl
recipes/ucsc-gmtime
recipes/ucsc-headrest
recipes/ucsc-hgbbidblink
recipes/ucsc-hgfakeagp
recipes/ucsc-hgfindspec
recipes/ucsc-hggoldgapgl
recipes/ucsc-hgloadbed
recipes/ucsc-hgloadchain
recipes/ucsc-hgloadmaf
recipes/ucsc-hgloadnet
recipes/ucsc-hgloadout
recipes/ucsc-hgloadoutjoined
recipes/ucsc-hgloadsqltab
recipes/ucsc-hgloadwiggle
recipes/ucsc-hgspeciesrna
recipes/ucsc-hgsqldump
recipes/ucsc-hgtrackdb
recipes/ucsc-hgvstovcf
recipes/ucsc-htmlcheck
recipes/ucsc-hubcheck
recipes/ucsc-hubpubliccheck
recipes/ucsc-ixixx
recipes/ucsc-lavtoaxt
recipes/ucsc-lavtopsl
recipes/ucsc-ldhggene
recipes/ucsc-liftup
recipes/ucsc-linestora
recipes/ucsc-localtime
recipes/ucsc-mafaddirows
recipes/ucsc-mafaddqrows
recipes/ucsc-mafcoverage
recipes/ucsc-maffetch
recipes/ucsc-maffilter
recipes/ucsc-maffrag
recipes/ucsc-maffrags
recipes/ucsc-mafgene
recipes/ucsc-mafmefirst
recipes/ucsc-maforder
recipes/ucsc-mafranges
recipes/ucsc-mafsinregion
recipes/ucsc-mafspecieslist
recipes/ucsc-mafspeciessubset
recipes/ucsc-mafsplit
recipes/ucsc-mafsplitpos
recipes/ucsc-maftoaxt
recipes/ucsc-maftobigmaf
recipes/ucsc-maftopsl
recipes/ucsc-maftosnpbed
recipes/ucsc-maketablelist
recipes/ucsc-maskoutfa
recipes/ucsc-mktime
recipes/ucsc-mrnatogene
recipes/ucsc-netchainsubset
recipes/ucsc-netclass
recipes/ucsc-netfilter
recipes/ucsc-netsplit
recipes/ucsc-netsyntenic
recipes/ucsc-nettoaxt
recipes/ucsc-nettobed
recipes/ucsc-newprog
recipes/ucsc-newpythonprog
recipes/ucsc-nibfrag
recipes/ucsc-nibsize
recipes/ucsc-oligomatch
recipes/ucsc-overlapselect
recipes/ucsc-para
recipes/ucsc-parafetch
recipes/ucsc-parahub
recipes/ucsc-parahubstop
recipes/ucsc-paranode
recipes/ucsc-paranodestart
recipes/ucsc-paranodestatus
recipes/ucsc-paranodestop