Update spaln to 2.4.13

[BiocondaBot]

Update spaln: 2.4.9 → 2.4.13

Info	Link or Description
Recipe	recipes/spaln (click to view/edit other files)
Summary	Map and align a set of cDNA/EST or protein sequences onto a genome
Home	http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/
Releases	https://github.com/ogotoh/spaln/tags
Author	@ogotoh

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This pull request was automatically generated (see docs).

[therealgenna]

Hi @ogotoh, bioconda build for spaln 2.4.13 fails apparently because standard IO functions don't recognize gzipped object pointers. We get blksrc.h errors like:

blksrc.h: In member function 'void MakeDbs::putsq(int)':
1blksrc.h:111:23: error: cannot convert 'gzFile' {aka 'gzFile_s*'} to 'FILE*'
  111 |   if (gzseq) fputc(c, gzseq);
      |                       ^~~~~
      |                       |
      |                       gzFile {aka gzFile_s*}

and similarly

blksrc.h:122:21: error: cannot convert 'gzFile' {aka 'gzFile_s*'} to 'FILE*'
blksrc.h:123:21: error: cannot convert 'gzFile' {aka 'gzFile_s*'} to 'FILE*'
blksrc.h:124:21: error: cannot convert 'gzFile' {aka 'gzFile_s*'} to 'FILE*'
blksrc.h:151:27: error: cannot convert 'gzFile' {aka 'gzFile_s*'} to 'FILE*'
blksrc.h:154:27: error: cannot convert 'gzFile' {aka 'gzFile_s*'} to 'FILE*'
blksrc.h:162:42: error: cannot convert 'gzFile' {aka 'gzFile_s*'} to 'FILE*'

We'll appreciate your suggestions/fixes!

[ogotoh]

Thank you for keeping spaln involved as a part of BioConda.

I have not changed the relevant files (blksrc.h, blksrc.cc) since the previous version (Ver2.4.12), while you seemed to have successfully compiled it. I guess that you might have changed the zlib library which would have some incompatibility with that I am using (zlib-1.2.12). Please let me know your current version, and if possible, please try earlier versions.

Osamu,

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差出人: therealgenna @.> 送信日時: 2022年9月20日 4:46 宛先: bioconda/bioconda-recipes @.> CC: 後藤修 @.>; Mention @.> 件名: Re: [bioconda/bioconda-recipes] Update spaln to 2.4.13 (PR #36968)

Hi @ogotohhttps://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fogotoh&data=05%7C01%7Co.gotoh%40aist.go.jp%7Ccb74ed73d8864e698c5b08da9a77af85%7C18a7fec8652f409b8369272d9ce80620%7C0%7C0%7C637992136080596695%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Oz5SGQAcujuRxurH%2BFjhrMD6W0HeESSX%2FvV4SpUPvGw%3D&reserved=0, bioconda build for spaln 2.4.13 fails apparently because standard IO functions don't recognize gzipped object pointers. We get blksrc.h errors like:

blksrc.h: In member function 'void MakeDbs::putsq(int)': 1blksrc.h:111:23: error: cannot convert 'gzFile' {aka 'gzFile_s*'} to 'FILE*' 111 | if (gzseq) fputc(c, gzseq); | ^~~~~ | | | gzFile {aka gzFile_s*}

and similarly

blksrc.h:122:21: error: cannot convert 'gzFile' {aka 'gzFile_s*'} to 'FILE*' blksrc.h:123:21: error: cannot convert 'gzFile' {aka 'gzFile_s*'} to 'FILE*' blksrc.h:124:21: error: cannot convert 'gzFile' {aka 'gzFile_s*'} to 'FILE*' blksrc.h:151:27: error: cannot convert 'gzFile' {aka 'gzFile_s*'} to 'FILE*' blksrc.h:154:27: error: cannot convert 'gzFile' {aka 'gzFile_s*'} to 'FILE*' blksrc.h:162:42: error: cannot convert 'gzFile' {aka 'gzFile_s*'} to 'FILE*'

We'll appreciate your suggestions/fixes!

— Reply to this email directly, view it on GitHubhttps://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fbioconda%2Fbioconda-recipes%2Fpull%2F36968%23issuecomment-1251472389&data=05%7C01%7Co.gotoh%40aist.go.jp%7Ccb74ed73d8864e698c5b08da9a77af85%7C18a7fec8652f409b8369272d9ce80620%7C0%7C0%7C637992136080596695%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=C8WnqYQNPkTaHlmFksgo9UaWKZCP3SpQn7xr8XQpX84%3D&reserved=0, or unsubscribehttps://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAH6C4LQB7ZC4VYDGXXXJO3LV7C7KJANCNFSM6AAAAAAQNBOVAU&data=05%7C01%7Co.gotoh%40aist.go.jp%7Ccb74ed73d8864e698c5b08da9a77af85%7C18a7fec8652f409b8369272d9ce80620%7C0%7C0%7C637992136080596695%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=xzOz9HZS5SNND6iG2mWfher84R6J95OnfKQwSeCGs24%3D&reserved=0. You are receiving this because you were mentioned.Message ID: @.***>

[therealgenna]

@ogotoh bioconda also uses zlib-1.2.12 ... Now when I tried it locally with a modified meta.yaml with an older zlib version for the host requirements it worked, even though I don't really understand why. So will PR this.

requirements:
   build:
     - make
     - {{ compiler('cxx') }}
   host:
     - perl
     - zlib=1.2.11
   run:
     - perl
     - zlib