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samtools: pull upstream fix for ncurses-6.3#147499

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SuperSandro2000 merged 1 commit intoNixOS:masterfrom
trofi:fix-samtools-for-ncurses-6.3
Nov 29, 2021
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samtools: pull upstream fix for ncurses-6.3#147499
SuperSandro2000 merged 1 commit intoNixOS:masterfrom
trofi:fix-samtools-for-ncurses-6.3

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@trofi trofi commented Nov 26, 2021

Without the fix build on ncurses-6.3 fails as:

bam_tview_curses.c:88:5: error: format not a string literal and no format arguments [-Werror=format-security]
   88 |     mvprintw(y,x,str);
      |     ^~~~~~~~

@trofi
samtools: pull upstream fix for ncurses-6.3
8147fb6 
Without the fix build on ncurses-6.3 fails as:

    bam_tview_curses.c:88:5: error: format not a string literal and no format arguments [-Werror=format-security]
       88 |     mvprintw(y,x,str);
          |     ^~~~~~~~
@trofi trofi force-pushed the fix-samtools-for-ncurses-6.3 branch from 7613f62 to 8147fb6 Compare November 26, 2021 13:02
@ofborg ofborg bot requested review from mimame and unode November 26, 2021 13:14
@ofborg ofborg bot added 10.rebuild-darwin: 1-10 This PR causes between 1 and 10 packages to rebuild on Darwin. 10.rebuild-linux: 11-100 This PR causes between 11 and 100 packages to rebuild on Linux. labels Nov 26, 2021
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unode commented Nov 26, 2021

samtools 1.14 is out since October. Shall we bump the version instead of cherry-picking patches?

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trofi commented Nov 26, 2021

Naive 1.13 -> 1.14 bump fails to build for me against current master as:

samtools> bam_import.c:180:35: error: 'FASTQ_OPT_NAME2' undeclared (first use in this function); did you mean 'FASTQ_OPT_RNUM'?
samtools>   180 |             hts_set_opt(fp_in[i], FASTQ_OPT_NAME2, 1);
samtools>       |                                   ^~~~~~~~~~~~~~~
samtools>       |                                   FASTQ_OPT_RNUM

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trofi commented Nov 26, 2021

Ah, it requires newer htslib as well. I'll give it a try.

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trofi commented Nov 26, 2021

Attempt to update htslib broke python3Packages.pysam. Attempt to update python3Packages.pysam broke python3Packages.cnvkit. I'm way out of my depth here. I'd suggest sorting update separately from ncurses compat.

@trofi trofi mentioned this pull request Nov 28, 2021
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@SuperSandro2000 SuperSandro2000 merged commit ebdd276 into NixOS:master Nov 29, 2021
@trofi trofi deleted the fix-samtools-for-ncurses-6.3 branch November 29, 2021 20:02
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10.rebuild-darwin: 1-10 This PR causes between 1 and 10 packages to rebuild on Darwin. 10.rebuild-linux: 11-100 This PR causes between 11 and 100 packages to rebuild on Linux.

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