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| author | Pjotr Prins | 2021-09-15 05:35:02 -0500 |
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| committer | Pjotr Prins | 2021-09-15 05:35:02 -0500 |
| commit | feaaf31062a77b986792a21b9df3cd617611fda4 (patch) | |
| tree | 3f4cf5926d5ebc29fc0c755661a9dd86075162ef | |
| parent | c1721156f5c17647833510be020b353537e4afa1 (diff) | |
| download | gn-gemtext-feaaf31062a77b986792a21b9df3cd617611fda4.tar.gz | |
Updated GN1 packages
| -rw-r--r-- | issues/genenetwork1/gn1-pairscan.gmi | 69 |
1 files changed, 69 insertions, 0 deletions
diff --git a/issues/genenetwork1/gn1-pairscan.gmi b/issues/genenetwork1/gn1-pairscan.gmi index b99b603..a47a3a3 100644 --- a/issues/genenetwork1/gn1-pairscan.gmi +++ b/issues/genenetwork1/gn1-pairscan.gmi @@ -1 +1,70 @@ # GN1 Pairscan + +Pair scan is not working because of an import issue. + +``` +Here is the error I get trying to run pair-scan. +Traceback (most recent call last): +File "/gnshare/gn/web/webqtl/cmdLine/webqtlCmdLine.py", line 79, in ? +from pairScan import DirectPlotPage +File "/gnshare/gn/web/webqtl/cmdLine/../pairScan/DirectPlotPage.py", line 32, +in ? +import direct +ImportError: No module named direct +``` + +# Tags + +* critical bug +* assigned: pjotrp + +# Notes + +Efraim included the module and wrote + +``` +from the traceback it looks like it's in production. + +from my gn1-python24-site-packages folder from lily there's a direct.so{,.bak} file so I'll start hunting around to see what I can make of it. +``` + +and a fix in guix-bioinformatics: + +``` +gn: Add python24-direct +``` + +it is not on Tux01, so let's update from + +``` +guix-past 4f5856f85578a04991dc646a06279d51f85973bf +guix-bioinformatics b08410a9944e677ef71267410b235ba869f3935f +``` + +and + +``` +gn1@tux01:~$ ~/opt/guix/bin/guix --version +guix (GNU Guix) 1.2.0-12.dffc918 +``` + +First update guix with + +``` +gn1@tux01:~$ ~/opt/guix/bin/guix pull -p ~/opt/guix-latest +``` + +Which got me the error Unbound variable: license:bsd-0. + +followed by the git repos above. + +The error changed into + +``` +Traceback (most recent call last): + File "/gnshare/gn/web/webqtl/cmdLine/webqtlCmdLine.py", line 81, in ? + page = DirectPlotPage.DirectPlotPage(fd) + File "/gnshare/gn/web/webqtl/cmdLine/../pairScan/DirectPlotPage.py", line 141, in __init__ + ResultFull, ResultInteract, ResultAdd = direct.permu(webqtlConfig.GENODIR, _vals, _strains, genofile + ".geno", 500) #XZ, 08/14/2008: add module name webqtlConfig +AttributeError: 'module' object has no attribute 'permu' +``` |