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HenrikBengtsson / CBI-software

A Scientific Software Stack for HPC (CentOS oriented)
https://wynton.ucsf.edu/hpc/software/software-repositories.html
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Wynton: Broken modules #112

Closed HenrikBengtsson closed 7 months ago

HenrikBengtsson commented 7 months ago 
[hb-test@dev3 wynton-tests]$ bin/wynton-tests lmod-repo-CBI
lmod-repo-CBI.bats

Checking 'lmod-repo-CBI' on 'rocky8' host 'dev3.wynton.ucsf.edu'
   'CBI' modules work                                                                                                                                                                     1/1
001/332 [ OK ] CBI-testing
002/332 [ OK ] apache-ant/1.10.12
003/332 [ OK ] asciigenome/1.15.0
004/332 [ OK ] asciigenome/1.16.0
005/332 [ OK ] asciigenome/1.17.0
006/332 [ OK ] bamutil/1.0.14
007/332 [ OK ] bat/0.23.0
008/332 [ OK ] bat/0.24.0
009/332 [ OK ] bats-assert/2.1.0
010/332 [ OK ] bats-core/1.10.0
011/332 [ OK ] bats-file/0.3.0
012/332 [ OK ] bats-support/0.3.0
013/332 [ OK ] bcftools/1.9
014/332 [ OK ] bcftools/1.10
015/332 [ OK ] bcftools/1.10.2
017/332 [ OK ] bcftools/1.13
018/332 [ OK ] bcftools/1.14
019/332 [ OK ] bcftools/1.15
020/332 [ OK ] bcftools/1.15.1
021/332 [ OK ] bcftools/1.16
022/332 [ OK ] bcftools/1.17
023/332 [ OK ] bcftools/1.18
024/332 [ OK ] bcl2fastq/2.20.0
025/332 [ OK ] bedops/2.4.36
026/332 [ OK ] bedops/2.4.37
027/332 [ OK ] bedops/2.4.38
028/332 [ OK ] bedops/2.4.39
029/332 [ OK ] bedops/2.4.40
030/332 [ OK ] bedops/2.4.41
031/332 [ OK ] bedtools2/2.26.0
032/332 [ OK ] bedtools2/2.28.0
033/332 [ OK ] bedtools2/2.29.1
034/332 [ OK ] bedtools2/2.29.2
035/332 [ OK ] bedtools2/2.30.0
036/332 [ OK ] blast/2.9.0
037/332 [ OK ] blast/2.10.1
038/332 [ OK ] blast/2.11.0
039/332 [ OK ] blast/2.12.0
040/332 [ OK ] blast/2.13.0
041/332 [ OK ] blast/2.14.0
042/332 [ OK ] blast/2.14.1
043/332 [ OK ] blat/36x4
044/332 [ OK ] blat/37x1
045/332 [ OK ] bowtie/1.2.3
046/332 [ OK ] bowtie/1.3.0
047/332 [ OK ] bowtie/1.3.1
048/332 [ OK ] bowtie2/2.3.5
049/332 [ OK ] bowtie2/2.3.5.1
050/332 [ OK ] bowtie2/2.4.1
051/332 [ OK ] bowtie2/2.4.2
052/332 [ OK ] bowtie2/2.4.4
053/332 [ OK ] bowtie2/2.4.5
054/332 [ OK ] bowtie2/2.5.0
055/332 [ OK ] bowtie2/2.5.1
056/332 [ OK ] bwa/0.7.17
057/332 [ OK ] byobu/5.133
058/332 [ OK ] cellranger/2.1.0
059/332 [ OK ] cellranger/3.0.2
060/332 [ OK ] cellranger/3.1.0
061/332 [ OK ] cellranger/4.0.0
062/332 [ OK ] cellranger/5.0.1
063/332 [ OK ] cellranger/6.1.1
064/332 [ OK ] cellranger/6.1.2
065/332 [ OK ] cellranger/7.0.0
066/332 [ OK ] cellranger/7.0.1
067/332 [ OK ] cellranger/7.1.0
068/332 cmake/3.26.3 ...Detected non-existing or inaccessible folder(s) in MANPATH: [n=1] /wynton/home/cbi/shared/software/CBI/cmake-3.26.3/share/man
068/332 [FAIL] cmake/3.26.3: non-existing or inaccessible MANPATH folder(s)
069/332 [ OK ] cmake/3.27.1
070/332 [ OK ] cmake/3.27.4
071/332 [ OK ] conda-stage/0.7.1
072/332 [ OK ] control-freec/11.5
073/332 [ OK ] control-freec/11.6
074/332 [ OK ] cufflinks/2.2.1
075/332 [ OK ] cutadapt/3.7
076/332 [ OK ] cutadapt/4.1
077/332 [ OK ] cutadapt/4.2
078/332 [ OK ] cutadapt/4.4
079/332 [ OK ] easycatfs/0.1.5
080/332 [ OK ] fastqc/0.11.8
081/332 [ OK ] fastqc/0.11.9
082/332 [ OK ] fastqc/0.12.1
083/332 [ OK ] fzf/0.42.0
084/332 [ OK ] fzf/0.43.0
085/332 [ OK ] gatk/4.1.0.0
086/332 [ OK ] gatk/4.1.2.0
087/332 [ OK ] gatk/4.1.3.0
088/332 [ OK ] gatk/4.1.4.0
089/332 [ OK ] gatk/4.1.6.0
090/332 [ OK ] gatk/4.1.7.0
091/332 [ OK ] gatk/4.1.9.0
092/332 [ OK ] gatk/4.2.2.0
093/332 [ OK ] gatk/4.2.4.1
094/332 [ OK ] gatk/4.2.5.0
095/332 [ OK ] gatk/4.2.6.0
096/332 [ OK ] gatk/4.2.6.1
097/332 [ OK ] gatk/4.3.0.0
098/332 [ OK ] gatk/4.4.0.0
099/332 [ OK ] gcta/1.26.0
100/332 [ OK ] gcta/1.92.3beta3
101/332 [ OK ] gcta/1.92.4beta
102/332 [ OK ] gcta/1.93.2beta
103/332 [ OK ] gcta/1.94.0beta
104/332 [ OK ] geos/3.5.2
105/332 [ OK ] geos/3.7.3
106/332 [ OK ] geos/3.8.1
107/332 [ OK ] geos/3.9.1
108/332 geos/3.9.2 ...Detected non-existing or inaccessible folder(s) in PATH: [n=1] /wynton/home/cbi/shared/software/CBI/geos-3.9.2/bin
Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /wynton/home/cbi/shared/software/CBI/geos-3.9.2/lib
Detected non-existing or inaccessible folder(s) in CPATH: [n=1] /wynton/home/cbi/shared/software/CBI/geos-3.9.2/include
108/332 [FAIL] geos/3.9.2: non-existing or inaccessible PATH LD_LIBRARY_PATH CPATH folder(s)
109/332 [ OK ] geos/3.9.3
110/332 [ OK ] geos/3.9.4
111/332 gistic2/2.0.23 ...Detected non-existing or inaccessible folder(s) in PATH: [n=1] /wynton/home/cbi/shared/software/CBI/gistic2-2.0.23 [no permission]
111/332 [FAIL] gistic2/2.0.23: non-existing or inaccessible PATH folder(s)
112/332 [ OK ] git-flow/1.12.3
113/332 [ OK ] glow/1.5.1
114/332 [ OK ] gping/1.14.0
115/332 [ OK ] gsl/2.6                  
116/332 [ OK ] gsl/2.7                  
117/332 [ OK ] hdf5/1.10.6              
118/332 [ OK ] hdf5/1.12.0              
119/332 [ OK ] hdf5/1.12.1              
120/332 [ OK ] hdf5/1.12.2              
121/332 [ OK ] hisat2/2.1.0             
122/332 [ OK ] hisat2/2.2.0             
123/332 [ OK ] htslib/1.9               
124/332 [ OK ] htslib/1.10.2            
125/332 [ OK ] htslib/1.11              
126/332 [ OK ] htslib/1.13              
127/332 [ OK ] htslib/1.14              
128/332 [ OK ] htslib/1.15              
129/332 [ OK ] htslib/1.15.1            
130/332 [ OK ] htslib/1.16              
131/332 [ OK ] htslib/1.17              
132/332 [ OK ] htslib/1.18
133/332 [ OK ] htstools/0.1.1
134/332 [ OK ] igv/2.4.19
135/332 [ OK ] igv/2.7.0
136/332 [ OK ] igv/2.7.2
137/332 [ OK ] igv/2.8.2
138/332 [ OK ] igv/2.8.6
139/332 [ OK ] igv/2.8.13
140/332 [ OK ] igv/2.9.1
141/332 [ OK ] igv/2.11.0
142/332 [ OK ] igv/2.11.9
143/332 [ OK ] igv/2.12.3
144/332 [ OK ] igv/2.13.0
145/332 [ OK ] igv/2.14.0
146/332 [ OK ] igv/2.14.1
147/332 [ OK ] igv/2.15.1
148/332 [ OK ] igv/2.15.4
149/332 [ OK ] igv/2.16.0
150/332 [ OK ] igv/2.16.1
151/332 [ OK ] igv/2.16.2
152/332 [ OK ] igvtools/2.4.19
153/332 [ OK ] jags/4.3.0
154/332 [ OK ] jags/4.3.1
155/332 [ OK ] jq/1.5
156/332 [ OK ] jq/1.7
157/332 [ OK ] kallisto/0.45.0
158/332 [ OK ] kallisto/0.45.1
159/332 [ OK ] kallisto/0.46.0
160/332 [ OK ] kallisto/0.46.1
161/332 [ OK ] kallisto/0.46.2
162/332 [ OK ] kallisto/0.50.0
163/332 [ OK ] markdownlint-cli/0.32.2
164/332 [ OK ] markdownlint-cli/0.35.0
165/332 [ OK ] mc/4.8.30
166/332 [FAIL] miniconda3-py39/4.12.0: cannot load
167/332 [ OK ] miniconda3/4.12.0-py39
168/332 [ OK ] miniconda3/22.11.1-1-py310
169/332 [ OK ] miniconda3/23.3.1-0-py39
170/332 [ OK ] miniconda3/23.5.2-0-py39
171/332 [ OK ] miniconda3/23.5.2-0-py310
172/332 [ OK ] miniconda3/23.5.2-0-py311
173/332 [ OK ] mutect/1.1.1
174/332 [ OK ] mutect/1.1.4
175/332 [FAIL] mutect/1.1.5: cannot load
176/332 [ OK ] ncdu/2.2.1                                                                                                
177/332 [ OK ] pandoc/3.1.8                                                                                            
178/332 [ OK ] pdfcrop/0.4b                                                                                                                                  
179/332 [ OK ] pdfcrop/1.42                                                                                              
180/332 [ OK ] picard/2.21.1                                                                                       
181/332 [ OK ] picard/2.21.4                                                                                                                                 
182/332 [ OK ] picard/2.22.2                                                                                             
183/332 [ OK ] picard/2.23.1                                                                                       
184/332 [ OK ] picard/2.24.0
185/332 [ OK ] picard/2.26.2
186/332 [ OK ] picard/2.26.10
187/332 [ OK ] picard/2.27.1
188/332 [ OK ] picard/2.27.4
189/332 [ OK ] picard/2.27.5
190/332 [ OK ] pindel/0.2.5b8
191/332 [ OK ] plink/1.07
192/332 [ OK ] plink/1.90b6.10
193/332 [ OK ] plink/1.90b6.16
194/332 [ OK ] plink/1.90b6.18
195/332 [ OK ] plink/1.90b6.21
196/332 [ OK ] plink/1.90b6.24
197/332 [ OK ] plink/1.90b6.25
198/332 [ OK ] plink/1.90b6.26
199/332 [ OK ] plink2/2.00a2LM
200/332 plink2/2.00a2.3 ...Detected non-existing or inaccessible folder(s) in PATH: [n=1] /wynton/home/cbi/shared/software/CBI/plink2-2.00a2.3
200/332 [FAIL] plink2/2.00a2.3: non-existing or inaccessible PATH folder(s)
201/332 [ OK ] plink2/2.00a3LM
202/332 [ OK ] port4me/0.6.0
203/332 [ OK ] proj/4.9.3
204/332 [ OK ] qtop/0.9.20161222
205/332 [ OK ] quarto/1.3.433
206/332 [ OK ] quarto/1.3.450
207/332 [ OK ] r-siteconfig/0.3
208/332 [ OK ] rclone/1.63.0
209/332 [ OK ] rclone/1.63.1
210/332 [ OK ] rclone/1.64.0
211/332 [ OK ] redis/7.0.12
212/332 [ OK ] redis/7.0.13
213/332 [ OK ] redis/7.2.1
214/332 [ OK ] restic/0.16.1
215/332 [ OK ] ripgrep/13.0.0
216/332 rstudio-server-controller/0.13.6 ...Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib/dyninst
Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib64/pkgconfig
216/332 [FAIL] rstudio-server-controller/0.13.6: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)
217/332 rstudio-server-controller/0.13.7 ...Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib/dyninst
Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib64/pkgconfig
217/332 [FAIL] rstudio-server-controller/0.13.7: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)
218/332 rstudio-server-controller/0.13.10 ...Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib/dyninst
Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib64/pkgconfig
218/332 [FAIL] rstudio-server-controller/0.13.10: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)
219/332 rstudio-server-controller/0.14.0 ...Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib/dyninst
Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib64/pkgconfig
219/332 [FAIL] rstudio-server-controller/0.14.0: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)
220/332 rstudio-server-controller/0.14.1 ...Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib/dyninst
Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib64/pkgconfig
220/332 [FAIL] rstudio-server-controller/0.14.1: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)
221/332 rstudio-server-controller/0.14.2 ...Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib/dyninst
Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib64/pkgconfig
221/332 [FAIL] rstudio-server-controller/0.14.2: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)
222/332 rstudio-server/2021.09.2-382 ...Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib/dyninst
Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib64/pkgconfig
222/332 [FAIL] rstudio-server/2021.09.2-382: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)
223/332 rstudio-server/2022.02.4-500 ...Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib/dyninst
Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib64/pkgconfig
223/332 [FAIL] rstudio-server/2022.02.4-500: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)
224/332 rstudio-server/2022.12.0-353 ...Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib/dyninst
Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib64/pkgconfig
224/332 [FAIL] rstudio-server/2022.12.0-353: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)
225/332 rstudio-server/2023.03.0-386 ...Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib/dyninst
Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib64/pkgconfig
225/332 [FAIL] rstudio-server/2023.03.0-386: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)
226/332 [FAIL] rstudio-server/2023.06.1-524: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)
227/332 rstudio-server/2023.06.2-561 ...Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib/dyninst
Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib64/pkgconfig
227/332 [FAIL] rstudio-server/2023.06.2-561: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)
228/332 rstudio-server/2023.09.0-463 ...Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib/dyninst
Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib64/pkgconfig
228/332 [FAIL] rstudio-server/2023.09.0-463: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)
229/332 rstudio/1.4.1103 ...Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib/dyninst
Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib64/pkgconfig
229/332 [FAIL] rstudio/1.4.1103: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)
230/332 rstudio/1.4.1717 ...Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib/dyninst
Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib64/pkgconfig
230/332 [FAIL] rstudio/1.4.1717: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)
231/332 rstudio/2021.09.0+351 ...Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib/dyninst
Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib64/pkgconfig
231/332 [FAIL] rstudio/2021.09.0+351: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)
232/332 rstudio/2021.09.1-372 ...Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib/dyninst
Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib64/pkgconfig
232/332 [FAIL] rstudio/2021.09.1-372: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)
233/332 rstudio/2021.09.2-382 ...Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib/dyninst
Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib64/pkgconfig
233/332 [FAIL] rstudio/2021.09.2-382: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)
234/332 rstudio/2022.02.1-461 ...Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib/dyninst
Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib64/pkgconfig
234/332 [FAIL] rstudio/2022.02.1-461: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)
235/332 rstudio/2022.07.2-576 ...Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib/dyninst
Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib64/pkgconfig
235/332 [FAIL] rstudio/2022.07.2-576: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)
236/332 rstudio/2022.12.0-353 ...Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib/dyninst
Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib64/pkgconfig
236/332 [FAIL] rstudio/2022.12.0-353: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)
237/332 rstudio/2023.06.1-524 ...Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib/dyninst
Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib64/pkgconfig
237/332 [FAIL] rstudio/2023.06.1-524: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)
238/332 [ OK ] salmon/1.3.0
239/332 [ OK ] salmon/1.4.0
240/332 [ OK ] salmon/1.5.2
241/332 [ OK ] salmon/1.6.0
242/332 [ OK ] salmon/1.8.0
243/332 [ OK ] salmon/1.9.0
244/332 [ OK ] salmon/1.10.0
245/332 [ OK ] samtools/1.9
246/332 [ OK ] samtools/1.10
247/332 [ OK ] samtools/1.11
248/332 [ OK ] samtools/1.13
249/332 [ OK ] samtools/1.14
250/332 [ OK ] samtools/1.15
251/332 [ OK ] samtools/1.15.1
252/332 [ OK ] samtools/1.16
253/332 [ OK ] samtools/1.16.1
254/332 [ OK ] samtools/1.17
255/332 [ OK ] samtools/1.18
256/332 [ OK ] shellcheck/0.8.0
257/332 [ OK ] shellcheck/0.9.0
258/332 [ OK ] snpeff/4.3t
259/332 [ OK ] snpeff/5.0c
260/332 [ OK ] snpeff/5.0e
261/332 [FAIL] snpeff/5.1e: cannot load
262/332 [FAIL] snpeff/5.1: cannot load
263/332 [ OK ] sratoolkit/2.10.0
264/332 [ OK ] sratoolkit/2.10.4
265/332 [ OK ] sratoolkit/2.10.5
266/332 [ OK ] sratoolkit/2.10.7
267/332 [ OK ] sratoolkit/2.10.8
268/332 [ OK ] sratoolkit/2.10.9
269/332 [ OK ] sratoolkit/2.11.0
270/332 [ OK ] sratoolkit/2.11.1
271/332 [ OK ] sratoolkit/2.11.2
272/332 [ OK ] sratoolkit/2.11.3
273/332 [ OK ] sratoolkit/3.0.0
274/332 [ OK ] sratoolkit/3.0.1
275/332 [ OK ] sratoolkit/3.0.2
276/332 [ OK ] sratoolkit/3.0.5
277/332 [ OK ] sratoolkit/3.0.6
278/332 [ OK ] sratoolkit/3.0.7
279/332 [ OK ] star/2.7.0e
280/332 [ OK ] star/2.7.0f
281/332 [ OK ] star/2.7.1a
282/332 [ OK ] star/2.7.2b
283/332 [ OK ] star/2.7.3a
284/332 [ OK ] star/2.7.5a
285/332 [ OK ] star/2.7.5c
286/332 [ OK ] star/2.7.7a
287/332 [ OK ] star/2.7.9a
288/332 [ OK ] star/2.7.10a
289/332 [ OK ] star/2.7.10b
290/332 [ OK ] star/2.7.11a
291/332 [ OK ] tmux/2.8
292/332 [ OK ] tophat/2.1.1
293/332 [ OK ] tree/2.1.1
294/332 [ OK ] trimgalore/0.6.7
295/332 [ OK ] trimgalore/0.6.10
296/332 [ OK ] up/0.4
297/332 [ OK ] varscan/2.4.2
298/332 [ OK ] varscan/2.4.6
299/332 [ OK ] vcf-validator/0.9.2
300/332 [ OK ] vcf-validator/0.9.3
301/332 [ OK ] vcf-validator/0.9.4
302/332 [ OK ] vcf-validator/0.9.5
303/332 [ OK ] vcftools/0.1.16
304/332 [ OK ] wynton-tools/0.2.0
305/332 [ OK ] x86-64-level/0.2.2
306/332 [ OK ] yq/4.35.1
307/332 [ OK ] yq/4.35.2
308/332 [ OK ] emacs/29.1
309/332 [ OK ] expect/5.45.4
310/332 [ OK ] htop/3.2.2
311/332 [ OK ] r/3.5.3
312/332 [ OK ] r/3.6.3
313/332 [ OK ] r/4.0.0-gcc10
314/332 [ OK ] r/4.0.0
315/332 [ OK ] r/4.0.5-gcc10
316/332 [ OK ] r/4.0.5
317/332 [ OK ] r/4.1.3-gcc8
318/332 [ OK ] r/4.1.3
319/332 r/4.2.0-gcc10 ...Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib/dyninst                                                                                               
Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib64/pkgconfig                                                                                                                    
319/332 [FAIL] r/4.2.0-gcc10: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)
320/332 r/4.2.0 ...Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib/dyninst                                                                                                     
Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib64/pkgconfig                                                                                                                    
320/332 [FAIL] r/4.2.0: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)
321/332 r/4.2.3-gcc10 ...Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib/dyninst                                                                                               
Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib64/pkgconfig                                                                                                                    
321/332 [FAIL] r/4.2.3-gcc10: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)
322/332 r/4.2.3 ...Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib/dyninst                                                                                                     
Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib64/pkgconfig                                                                                                                    
322/332 [FAIL] r/4.2.3: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)                                                                                                                                               
323/332 [ OK ] r/4.3.0-gcc10                                                                                                                                                                                                                 
324/332 [ OK ] r/4.3.0                                                                                                                                                                                                                       
325/332 r/4.3.1-gcc10 ...Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib/dyninst                                                                                               
Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib64/pkgconfig                                                                                                                    
325/332 [FAIL] r/4.3.1-gcc10: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)
326/332 r/4.3.1 ...Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib/dyninst                                                                                                     
Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib64/pkgconfig                                                                                                                    
326/332 [FAIL] r/4.3.1: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)
327/332 scl-gcc-toolset/9 ...Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /opt/rh/gcc-toolset-9/root/usr/lib/dyninst
Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-9/root/usr/lib64/pkgconfig
327/332 [FAIL] scl-gcc-toolset/9: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)
328/332 scl-gcc-toolset/10 ...Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib/dyninst
Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-10/root/usr/lib64/pkgconfig
328/332 [FAIL] scl-gcc-toolset/10: non-existing or inaccessible LD_LIBRARY_PATH PKG_CONFIG_PATH folder(s)
329/332 scl-gcc-toolset/11 ...Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-11/root/usr/lib64/pkgconfig
329/332 [FAIL] scl-gcc-toolset/11: non-existing or inaccessible PKG_CONFIG_PATH folder(s)
330/332 scl-gcc-toolset/12 ...Detected non-existing or inaccessible folder(s) in PKG_CONFIG_PATH: [n=1] /opt/rh/gcc-toolset-12/root/usr/lib64/pkgconfig
330/332 [FAIL] scl-gcc-toolset/12: non-existing or inaccessible PKG_CONFIG_PATH folder(s)
331/332 [ OK ] sqlite/3.43.0
332/332 [ OK ] sqlite/3.43.2

   (from function `fail' in file /wynton/home/cbi/shared/software/CBI/bats-support-0.3.0/src/error.bash, line 40,
    from function `assert_lmod_repo' in file /wynton/home/cbi/hb/shared/repositories/wynton-tests/tests/incl/utils.sh, line 329,
    in test file /wynton/home/cbi/hb/shared/repositories/wynton-tests/tests/lmod-repo-CBI.bats, line 12)
     `assert_lmod_repo "CBI"' failed
   MODULE WARNING: samtools 1.11 has a bug that results in valid but incorrect CIGAR strings. Because of this, it is recommended to use an older or a newer                                                                                  
   version instead. For details, see https://github.com/samtools/htslib/issues/1236
   Lmod has detected the following error: The following module(s) are unknown: "openjdk/18"

   Please check the spelling or version number. Also try "module spider ..."
   It is also possible your cache file is out-of-date; it may help to try:
     $ module --ignore_cache load "openjdk/18"

   Also make sure that all modulefiles written in TCL start with the string #%Module

   Executing this command requires loading "openjdk/18" which failed while processing the following module(s):

       Module fullname  Module Filename
       ---------------  ---------------
       snpeff/5.1e      /wynton/home/cbi/shared/modulefiles/CBI/snpeff/5.1e.lua

   Lmod has detected the following error: The following module(s) are unknown: "openjdk/18"

   Please check the spelling or version number. Also try "module spider ..."
   It is also possible your cache file is out-of-date; it may help to try:
     $ module --ignore_cache load "openjdk/18"

   Also make sure that all modulefiles written in TCL start with the string #%Module

   Executing this command requires loading "openjdk/18" which failed while processing the following module(s):

       Module fullname  Module Filename
       ---------------  ---------------
       snpeff/5.1       /wynton/home/cbi/shared/modulefiles/CBI/snpeff/5.1.lua

   Failed modules: [n=35] plink2/2.00a2.3 rstudio-server-controller/0.13.6 rstudio-server-controller/0.13.7 rstudio-server-controller/0.13.10 rstudio-server-controller/0.14.0 rstudio-server-controller/0.14.1 rstudio-server-controller/0.14
.2 rstudio-server/2021.09.2-382 rstudio-server/2022.02.4-500 rstudio-server/2022.12.0-353 rstudio-server/2023.03.0-386 rstudio-server/2023.06.1-524 rstudio-server/2023.06.2-561 rstudio-server/2023.09.0-463 rstudio/1.4.1103 rstudio/1.4.171
7 rstudio/2021.09.0+351 rstudio/2021.09.1-372 rstudio/2021.09.2-382 rstudio/2022.02.1-461 rstudio/2022.07.2-576 rstudio/2022.12.0-353 rstudio/2023.06.1-524 snpeff/5.1e snpeff/5.1 r/4.2.0-gcc10 r/4.2.0 r/4.2.3-gcc10 r/4.2.3 r/4.3.1-gcc10 r
/4.3.1 scl-gcc-toolset/9 scl-gcc-toolset/10 scl-gcc-toolset/11 scl-gcc-toolset/12

1 test, 1 failure
HenrikBengtsson commented 7 months ago

Fixed:

068/332 cmake/3.26.3 ...Detected non-existing or inaccessible folder(s) in MANPATH: [n=1] /wynton/home/cbi/shared/software/CBI/cmake-3.26.3/share/man
068/332 [FAIL] cmake/3.26.3: non-existing or inaccessible MANPATH folder(s)

by reinstalling module.

HenrikBengtsson commented 7 months ago

Fixed

111/332 gistic2/2.0.23 ...Detected non-existing or inaccessible folder(s) in PATH: [n=1] /wynton/home/cbi/shared/software/CBI/gistic2-2.0.23 [no permission]
111/332 [FAIL] gistic2/2.0.23: non-existing or inaccessible PATH folder(s)

by reinstalling gistic2 after fixing #111.

HenrikBengtsson commented 7 months ago

Fixed:

200/332 plink2/2.00a2.3 ...Detected non-existing or inaccessible folder(s) in PATH: [n=1] /wynton/home/cbi/shared/software/CBI/plink2-2.00a2.3
200/332 [FAIL] plink2/2.00a2.3: non-existing or inaccessible PATH folder(s)

by make remove VERSION=2.00a2.3.

HenrikBengtsson commented 7 months ago

Fixed

108/332 geos/3.9.2 ...Detected non-existing or inaccessible folder(s) in PATH: [n=1] /wynton/home/cbi/shared/software/CBI/geos-3.9.2/bin
Detected non-existing or inaccessible folder(s) in LD_LIBRARY_PATH: [n=1] /wynton/home/cbi/shared/software/CBI/geos-3.9.2/lib
Detected non-existing or inaccessible folder(s) in CPATH: [n=1] /wynton/home/cbi/shared/software/CBI/geos-3.9.2/include
108/332 [FAIL] geos/3.9.2: non-existing or inaccessible PATH LD_LIBRARY_PATH CPATH folder(s)

by remove half-installed version; only the module existed (make remove VERSION=3.9.2).

HenrikBengtsson commented 7 months ago

UPDATE:

[hb-test@dev3 ~]$ /wynton/home/cbi/hb/shared/repositories/wynton-tests/bin/wynton-tests lmod-repo-CBI
lmod-repo-CBI.bats         

Checking 'lmod-repo-CBI' on 'rocky8' host 'dev3.wynton.ucsf.edu'
'CBI' modules work
001/331 [ OK ] CBI-testing  
002/331 [ OK ] apache-ant/1.10.12
003/331 [ OK ] asciigenome/1.15.0
004/331 [ OK ] asciigenome/1.16.0
005/331 [ OK ] asciigenome/1.17.0
006/331 [ OK ] bamutil/1.0.14
007/331 [ OK ] bat/0.23.0   
008/331 [ OK ] bat/0.24.0     
009/331 [ OK ] bats-assert/2.1.0
010/331 [ OK ] bats-core/1.10.0
011/331 [ OK ] bats-file/0.3.0
012/331 [ OK ] bats-support/0.3.0
013/331 [ OK ] bcftools/1.9    
014/331 [ OK ] bcftools/1.10   
015/331 [ OK ] bcftools/1.10.2
016/331 [ OK ] bcftools/1.11
017/331 [ OK ] bcftools/1.13
018/331 [ OK ] bcftools/1.14           
019/331 [ OK ] bcftools/1.15          
020/331 [ OK ] bcftools/1.15.1  
021/331 [ OK ] bcftools/1.16    
022/331 [ OK ] bcftools/1.17    
023/331 [ OK ] bcftools/1.18    
024/331 [ OK ] bcl2fastq/2.20.0 
025/331 [ OK ] bedops/2.4.36    
026/331 [ OK ] bedops/2.4.37    
027/331 [ OK ] bedops/2.4.38
028/331 [ OK ] bedops/2.4.39    
029/331 [ OK ] bedops/2.4.40    
030/331 [ OK ] bedops/2.4.41   
031/331 [ OK ] bedtools2/2.26.0
032/331 [ OK ] bedtools2/2.28.0
033/331 [ OK ] bedtools2/2.29.1
034/331 [ OK ] bedtools2/2.29.2
035/331 [ OK ] bedtools2/2.30.0
036/331 [ OK ] blast/2.9.0    
037/331 [ OK ] blast/2.10.1   
038/331 [ OK ] blast/2.11.0   
039/331 [ OK ] blast/2.12.0   
040/331 [ OK ] blast/2.13.0   
041/331 [ OK ] blast/2.14.0   
042/331 [ OK ] blast/2.14.1           
043/331 [ OK ] blat/36x4              
044/331 [ OK ] blat/37x1  
045/331 [ OK ] bowtie/1.2.3                       
046/331 [ OK ] bowtie/1.3.0          
047/331 [ OK ] bowtie/1.3.1              
048/331 [ OK ] bowtie2/2.3.5           
049/331 [ OK ] bowtie2/2.3.5.1         
050/331 [ OK ] bowtie2/2.4.1            
051/331 [ OK ] bowtie2/2.4.2            
052/331 [ OK ] bowtie2/2.4.4            
053/331 [ OK ] bowtie2/2.4.5            
054/331 [ OK ] bowtie2/2.5.0            
055/331 [ OK ] bowtie2/2.5.1
056/331 [ OK ] bwa/0.7.17         
057/331 [ OK ] byobu/5.133        
058/331 [ OK ] cellranger/2.1.0   
059/331 [ OK ] cellranger/3.0.2   
060/331 [ OK ] cellranger/3.1.0
061/331 [ OK ] cellranger/4.0.0  
062/331 [ OK ] cellranger/5.0.1  
063/331 [ OK ] cellranger/6.1.1
064/331 [ OK ] cellranger/6.1.2
065/331 [ OK ] cellranger/7.0.0
066/331 [ OK ] cellranger/7.0.1
067/331 [ OK ] cellranger/7.1.0
068/331 [ OK ] cmake/3.26.3 
069/331 [ OK ] cmake/3.27.1  
070/331 [ OK ] cmake/3.27.4 
071/331 [ OK ] cmake/3.27.7   
072/331 [ OK ] conda-stage/0.7.1
073/331 [ OK ] control-freec/11.5
074/331 [ OK ] control-freec/11.6
075/331 [ OK ] cufflinks/2.2.1
076/331 [ OK ] cutadapt/3.7   
077/331 [ OK ] cutadapt/4.1   
078/331 [ OK ] cutadapt/4.2   
079/331 [ OK ] cutadapt/4.4   
080/331 [ OK ] easycatfs/0.1.5
081/331 [ OK ] fastqc/0.11.8
082/331 [ OK ] fastqc/0.11.9    
083/331 [ OK ] fastqc/0.12.1 
084/331 [ OK ] fzf/0.42.0       
085/331 [ OK ] fzf/0.43.0        
084/331 [ OK ] fzf/0.42.0
085/331 [ OK ] fzf/0.43.0
086/331 [ OK ] gatk/4.1.0.0
087/331 [ OK ] gatk/4.1.2.0
088/331 [ OK ] gatk/4.1.3.0
089/331 [ OK ] gatk/4.1.4.0
090/331 [ OK ] gatk/4.1.6.0
091/331 [ OK ] gatk/4.1.7.0
092/331 [ OK ] gatk/4.1.9.0
093/331 [ OK ] gatk/4.2.2.0
094/331 [ OK ] gatk/4.2.4.1
095/331 [ OK ] gatk/4.2.5.0
096/331 [ OK ] gatk/4.2.6.0
097/331 [ OK ] gatk/4.2.6.1
098/331 [ OK ] gatk/4.3.0.0
099/331 [ OK ] gatk/4.4.0.0
100/331 [ OK ] gcta/1.26.0
101/331 [ OK ] gcta/1.92.3beta3
102/331 [ OK ] gcta/1.92.4beta
103/331 [ OK ] gcta/1.93.2beta
104/331 [ OK ] gcta/1.94.0beta
105/331 [ OK ] geos/3.5.2
106/331 [ OK ] geos/3.7.3
107/331 [ OK ] geos/3.8.1
108/331 [ OK ] geos/3.9.1
109/331 [ OK ] geos/3.9.3
110/331 [ OK ] geos/3.9.4
111/331 [ OK ] gistic2/2.0.23
112/331 [ OK ] git-flow/1.12.3
113/331 [ OK ] glow/1.5.1
114/331 [ OK ] gping/1.14.0
115/331 [ OK ] gsl/2.6
116/331 [ OK ] gsl/2.7
117/331 [ OK ] hdf5/1.10.6
118/331 [ OK ] hdf5/1.12.0
119/331 [ OK ] hdf5/1.12.1
120/331 [ OK ] hdf5/1.12.2
121/331 [ OK ] hisat2/2.1.0
122/331 [ OK ] hisat2/2.2.0
123/331 [ OK ] htslib/1.9
124/331 [ OK ] htslib/1.10.2
125/331 [ OK ] htslib/1.11
126/331 [ OK ] htslib/1.13
127/331 [ OK ] htslib/1.14
128/331 [ OK ] htslib/1.15
129/331 [ OK ] htslib/1.15.1
130/331 [ OK ] htslib/1.16
131/331 [ OK ] htslib/1.17
132/331 [ OK ] htslib/1.18
133/331 [ OK ] htstools/0.1.1
134/331 [ OK ] igv/2.4.19
135/331 [ OK ] igv/2.7.0
136/331 [ OK ] igv/2.7.2
137/331 [ OK ] igv/2.8.2
138/331 [ OK ] igv/2.8.6
139/331 [ OK ] igv/2.8.13
140/331 [ OK ] igv/2.9.1
141/331 [ OK ] igv/2.11.0
142/331 [ OK ] igv/2.11.9
143/331 [ OK ] igv/2.12.3
144/331 [ OK ] igv/2.13.0
145/331 [ OK ] igv/2.14.0
146/331 [ OK ] igv/2.14.1
147/331 [ OK ] igv/2.15.1
148/331 [ OK ] igv/2.15.4
149/331 [ OK ] igv/2.16.0
150/331 [ OK ] igv/2.16.1
151/331 [ OK ] igv/2.16.2
152/331 [ OK ] igvtools/2.4.19
153/331 [ OK ] jags/4.3.0
154/331 [ OK ] jags/4.3.1
155/331 [ OK ] jq/1.5
156/331 [ OK ] jq/1.7
157/331 [ OK ] kallisto/0.45.0
158/331 [ OK ] kallisto/0.45.1
159/331 [ OK ] kallisto/0.46.0
160/331 [ OK ] kallisto/0.46.1
161/331 [ OK ] kallisto/0.46.2
162/331 [ OK ] kallisto/0.50.0
163/331 [ OK ] markdownlint-cli/0.32.2
164/331 [ OK ] markdownlint-cli/0.35.0
165/331 [ OK ] mc/4.8.30
166/331 [FAIL] miniconda3-py39/4.12.0: cannot load
167/331 [ OK ] miniconda3/4.12.0-py39
168/331 [ OK ] miniconda3/22.11.1-1-py310
169/331 [ OK ] miniconda3/23.3.1-0-py39
170/331 [ OK ] miniconda3/23.5.2-0-py39
171/331 [ OK ] miniconda3/23.5.2-0-py310
172/331 [ OK ] miniconda3/23.5.2-0-py311
173/331 [FAIL] mutect/1.1.1: cannot load
174/331 [FAIL] mutect/1.1.4: cannot load
175/331 [FAIL] mutect/1.1.5: cannot load
176/331 [ OK ] ncdu/2.2.1
177/331 [ OK ] pandoc/3.1.8
178/331 [ OK ] pdfcrop/0.4b
179/331 [ OK ] pdfcrop/1.42
180/331 [ OK ] picard/2.21.1
181/331 [ OK ] picard/2.21.4
182/331 [ OK ] picard/2.22.2
183/331 [ OK ] picard/2.23.1
184/331 [ OK ] picard/2.24.0
185/331 [ OK ] picard/2.26.2
186/331 [ OK ] picard/2.26.10
187/331 [ OK ] picard/2.27.1
188/331 [ OK ] picard/2.27.4
189/331 [ OK ] picard/2.27.5
190/331 [ OK ] pindel/0.2.5b8
191/331 [ OK ] plink/1.07
192/331 [ OK ] plink/1.90b6.10
193/331 [ OK ] plink/1.90b6.16
194/331 [ OK ] plink/1.90b6.18
195/331 [ OK ] plink/1.90b6.21
196/331 [ OK ] plink/1.90b6.24
197/331 [ OK ] plink/1.90b6.25
198/331 [ OK ] plink/1.90b6.26
199/331 [ OK ] plink2/2.00a2LM
200/331 [ OK ] plink2/2.00a3LM
201/331 [ OK ] port4me/0.6.0
202/331 [ OK ] proj/4.9.3
203/331 [ OK ] qtop/0.9.20161222
204/331 [ OK ] quarto/1.3.433
205/331 [ OK ] quarto/1.3.450
206/331 [ OK ] r-siteconfig/0.3
207/331 [ OK ] rclone/1.63.0
208/331 [ OK ] rclone/1.63.1
209/331 [ OK ] rclone/1.64.0
324/331 [ OK ] r/4.3.1-gcc10
325/331 [ OK ] r/4.3.1
326/331 [ OK ] scl-gcc-toolset/9
327/331 [ OK ] scl-gcc-toolset/10
328/331 [ OK ] scl-gcc-toolset/11
329/331 [ OK ] scl-gcc-toolset/12
330/331 [ OK ] sqlite/3.43.0
331/331 [ OK ] sqlite/3.43.2
   (from function `fail' in file /wynton/home/cbi/shared/software/CBI/bats-support-0.3.0/src/error.bash, line 40,
    from function `assert_lmod_repo' in file /wynton/home/cbi/hb/shared/repositories/wynton-tests/tests/incl/utils.sh, line 361,
    in test file /wynton/home/cbi/hb/shared/repositories/wynton-tests/tests/lmod-repo-CBI.bats, line 12)
     `assert_lmod_repo "CBI"' failed
   MODULE WARNING: bcftools 1.11 has a bug that results in valid but incorrect CIGAR strings. Because of this, it is recommended to use an older or a newer version instead. For details, see https://github.com/samtools/htslib/issues/1236
   MODULE WARNING: htslib 1.11 has a bug that results in valid but incorrect CIGAR strings. Because of this, it is recommended to use an older or a newer version instead. For details, see https://github.com/samtools/htslib/issues/1236
   Lmod has detected the following error: The CBI 'miniconda3-py39/4.12.0' module has been renamed to 'miniconda3/4.12.0-py39'; please use the latter instead
   While processing the following module(s):
       Module fullname         Module Filename
       ---------------         ---------------
       miniconda3-py39/4.12.0  /wynton/home/cbi/shared/modulefiles/CBI/miniconda3-py39/4.12.0.lua

   Note: the module "miniconda3-py39/4.12.0" cannot be unloaded because it was not loaded.

   Lmod Warning: mutect/1.1.1 requires Java v1.7, but you are running openjdk version "17.0.9" 2023-10-17 LTS
   While processing the following module(s):
       Module fullname  Module Filename
       ---------------  ---------------
       mutect/1.1.1     /wynton/home/cbi/shared/modulefiles/CBI/mutect/1.1.1.lua

   Lmod Warning: mutect/1.1.1 requires Java v1.7, but you are running openjdk version "17.0.9" 2023-10-17 LTS
   While processing the following module(s):
       Module fullname  Module Filename
       ---------------  ---------------
       mutect/1.1.1     /wynton/home/cbi/shared/modulefiles/CBI/mutect/1.1.1.lua

   Lmod Warning: mutect/1.1.1 requires Java v1.7, but you are running openjdk version "17.0.9" 2023-10-17 LTS
   While processing the following module(s):
       Module fullname  Module Filename
       ---------------  ---------------
       mutect/1.1.1     /wynton/home/cbi/shared/modulefiles/CBI/mutect/1.1.1.lua

   Lmod Warning: mutect/1.1.4 requires Java v1.7, but you are running openjdk version "17.0.9" 2023-10-17 LTS
   While processing the following module(s):
       Module fullname  Module Filename
       ---------------  ---------------
       mutect/1.1.4     /wynton/home/cbi/shared/modulefiles/CBI/mutect/1.1.4.lua

   Lmod Warning: mutect/1.1.4 requires Java v1.7, but you are running openjdk version "17.0.9" 2023-10-17 LTS
   While processing the following module(s):
       Module fullname  Module Filename
       ---------------  ---------------
       mutect/1.1.4     /wynton/home/cbi/shared/modulefiles/CBI/mutect/1.1.4.lua

   Lmod Warning: mutect/1.1.4 requires Java v1.7, but you are running openjdk version "17.0.9" 2023-10-17 LTS
   While processing the following module(s):
       Module fullname  Module Filename
       ---------------  ---------------
       mutect/1.1.4     /wynton/home/cbi/shared/modulefiles/CBI/mutect/1.1.4.lua

   Lmod Warning: mutect/1.1.5 requires Java v1.7, but you are running openjdk version "17.0.9" 2023-10-17 LTS
   While processing the following module(s):
       Module fullname  Module Filename
       ---------------  ---------------
       mutect/1.1.5     /wynton/home/cbi/shared/modulefiles/CBI/mutect/1.1.5.lua

   Lmod Warning: mutect/1.1.5 requires Java v1.7, but you are running openjdk version "17.0.9" 2023-10-17 LTS
   While processing the following module(s):
       Module fullname  Module Filename
       ---------------  ---------------
       mutect/1.1.5     /wynton/home/cbi/shared/modulefiles/CBI/mutect/1.1.5.lua

   Lmod Warning: mutect/1.1.5 requires Java v1.7, but you are running openjdk version "17.0.9" 2023-10-17 LTS
   While processing the following module(s):
       Module fullname  Module Filename
       ---------------  ---------------
       mutect/1.1.5     /wynton/home/cbi/shared/modulefiles/CBI/mutect/1.1.5.lua

   The following have been reloaded with a version change:
     1) openjdk/17 => openjdk/1.8.0

   MODULE WARNING: samtools 1.11 has a bug that results in valid but incorrect CIGAR strings. Because of this, it is recommended to use an older or a newer version instead. For details, see https://github.com/samtools/htslib/issues/1236
   Lmod has detected the following error: The following module(s) are unknown: "openjdk/18"

   Please check the spelling or version number. Also try "module spider ..."
   It is also possible your cache file is out-of-date; it may help to try:
     $ module --ignore_cache load "openjdk/18"

   Also make sure that all modulefiles written in TCL start with the string #%Module

   Executing this command requires loading "openjdk/18" which failed while processing the following module(s):

       Module fullname  Module Filename
       ---------------  ---------------
       snpeff/5.1e      /wynton/home/cbi/shared/modulefiles/CBI/snpeff/5.1e.lua

   Note: the module "snpeff/5.1e" cannot be unloaded because it was not loaded.

   Lmod has detected the following error: The following module(s) are unknown: "openjdk/18"

   Please check the spelling or version number. Also try "module spider ..."
   It is also possible your cache file is out-of-date; it may help to try:
     $ module --ignore_cache load "openjdk/18"

   Also make sure that all modulefiles written in TCL start with the string #%Module

   Executing this command requires loading "openjdk/18" which failed while processing the following module(s):

       Module fullname  Module Filename
       ---------------  ---------------
       snpeff/5.1       /wynton/home/cbi/shared/modulefiles/CBI/snpeff/5.1.lua

   Note: the module "snpeff/5.1" cannot be unloaded because it was not loaded.

   Failed modules: [n=6] miniconda3-py39/4.12.0 mutect/1.1.1 mutect/1.1.4 mutect/1.1.5 snpeff/5.1e snpeff/5.1

1 test, 1 failure
HenrikBengtsson commented 7 months ago

All the non-OK modules behaves as expected, because ...

The following is expected because it is defunct:

166/331 [FAIL] miniconda3-py39/4.12.0: cannot load

The following fail because they require Java (== 1.7), which is not available:

173/331 [FAIL] mutect/1.1.1: cannot load
174/331 [FAIL] mutect/1.1.4: cannot load
175/331 [FAIL] mutect/1.1.5: cannot load
HenrikBengtsson commented 7 months ago

UPDATE:

[hb-test@dev3 ~]$ /wynton/home/cbi/hb/shared/repositories/wynton-tests/bin/wynton-tests lmod-repo-CBI
lmod-repo-CBI.bats

Checking 'lmod-repo-CBI' on 'rocky8' host 'dev3.wynton.ucsf.edu'
'CBI' modules work
1/1
001/331 [ OK ] CBI-testing
002/331 [ OK ] apache-ant/1.10.12
003/331 [ OK ] asciigenome/1.15.0
004/331 [ OK ] asciigenome/1.16.0
005/331 [ OK ] asciigenome/1.17.0
006/331 [ OK ] bamutil/1.0.14
007/331 [ OK ] bat/0.23.0
008/331 [ OK ] bat/0.24.0
009/331 [ OK ] bats-assert/2.1.0
010/331 [ OK ] bats-core/1.10.0
011/331 [ OK ] bats-file/0.3.0
012/331 [ OK ] bats-support/0.3.0
013/331 [ OK ] bcftools/1.9
014/331 [ OK ] bcftools/1.10
015/331 [ OK ] bcftools/1.10.2
016/331 [ OK ] bcftools/1.11
017/331 [ OK ] bcftools/1.13
018/331 [ OK ] bcftools/1.14
019/331 [ OK ] bcftools/1.15
020/331 [ OK ] bcftools/1.15.1
021/331 [ OK ] bcftools/1.16
022/331 [ OK ] bcftools/1.17
023/331 [ OK ] bcftools/1.18
024/331 [ OK ] bcl2fastq/2.20.0
025/331 [ OK ] bedops/2.4.36
026/331 [ OK ] bedops/2.4.37
027/331 [ OK ] bedops/2.4.38
028/331 [ OK ] bedops/2.4.39
029/331 [ OK ] bedops/2.4.40
030/331 [ OK ] bedops/2.4.41
031/331 [ OK ] bedtools2/2.26.0
032/331 [ OK ] bedtools2/2.28.0
033/331 [ OK ] bedtools2/2.29.1
034/331 [ OK ] bedtools2/2.29.2
035/331 [ OK ] bedtools2/2.30.0
036/331 [ OK ] blast/2.9.0
037/331 [ OK ] blast/2.10.1
038/331 [ OK ] blast/2.11.0
039/331 [ OK ] blast/2.12.0
040/331 [ OK ] blast/2.13.0
041/331 [ OK ] blast/2.14.0
042/331 [ OK ] blast/2.14.1
043/331 [ OK ] blat/36x4
044/331 [ OK ] blat/37x1
045/331 [ OK ] bowtie/1.2.3
046/331 [ OK ] bowtie/1.3.0
047/331 [ OK ] bowtie/1.3.1
048/331 [ OK ] bowtie2/2.3.5
049/331 [ OK ] bowtie2/2.3.5.1
050/331 [ OK ] bowtie2/2.4.1
051/331 [ OK ] bowtie2/2.4.2
052/331 [ OK ] bowtie2/2.4.4
053/331 [ OK ] bowtie2/2.4.5
054/331 [ OK ] bowtie2/2.5.0
055/331 [ OK ] bowtie2/2.5.1
056/331 [ OK ] bwa/0.7.17
057/331 [ OK ] byobu/5.133
058/331 [ OK ] cellranger/2.1.0
059/331 [ OK ] cellranger/3.0.2
060/331 [ OK ] cellranger/3.1.0
061/331 [ OK ] cellranger/4.0.0
062/331 [ OK ] cellranger/5.0.1
063/331 [ OK ] cellranger/6.1.1
064/331 [ OK ] cellranger/6.1.2
065/331 [ OK ] cellranger/7.0.0
066/331 [ OK ] cellranger/7.0.1
067/331 [ OK ] cellranger/7.1.0
068/331 [ OK ] cmake/3.26.3
069/331 [ OK ] cmake/3.27.1
070/331 [ OK ] cmake/3.27.4
071/331 [ OK ] cmake/3.27.7
072/331 [ OK ] conda-stage/0.7.1
073/331 [ OK ] control-freec/11.5
074/331 [ OK ] control-freec/11.6
075/331 [ OK ] cufflinks/2.2.1
076/331 [ OK ] cutadapt/3.7
077/331 [ OK ] cutadapt/4.1
078/331 [ OK ] cutadapt/4.2
079/331 [ OK ] cutadapt/4.4
080/331 [ OK ] easycatfs/0.1.5
081/331 [ OK ] fastqc/0.11.8
082/331 [ OK ] fastqc/0.11.9
083/331 [ OK ] fastqc/0.12.1
084/331 [ OK ] fzf/0.42.0
085/331 [ OK ] fzf/0.43.0
086/331 [ OK ] gatk/4.1.0.0
087/331 [ OK ] gatk/4.1.2.0
088/331 [ OK ] gatk/4.1.3.0
089/331 [ OK ] gatk/4.1.4.0
090/331 [ OK ] gatk/4.1.6.0
091/331 [ OK ] gatk/4.1.7.0
092/331 [ OK ] gatk/4.1.9.0
093/331 [ OK ] gatk/4.2.2.0
094/331 [ OK ] gatk/4.2.4.1
095/331 [ OK ] gatk/4.2.5.0
096/331 [ OK ] gatk/4.2.6.0
097/331 [ OK ] gatk/4.2.6.1
098/331 [ OK ] gatk/4.3.0.0
099/331 [ OK ] gatk/4.4.0.0
100/331 [ OK ] gcta/1.26.0
101/331 [ OK ] gcta/1.92.3beta3
102/331 [ OK ] gcta/1.92.4beta
103/331 [ OK ] gcta/1.93.2beta
104/331 [ OK ] gcta/1.94.0beta
105/331 [ OK ] geos/3.5.2
106/331 [ OK ] geos/3.7.3
107/331 [ OK ] geos/3.8.1
108/331 [ OK ] geos/3.9.1
109/331 [ OK ] geos/3.9.3
110/331 [ OK ] geos/3.9.4
111/331 [ OK ] gistic2/2.0.23
112/331 [ OK ] git-flow/1.12.3
113/331 [ OK ] glow/1.5.1
114/331 [ OK ] gping/1.14.0
115/331 [ OK ] gsl/2.6
116/331 [ OK ] gsl/2.7
117/331 [ OK ] hdf5/1.10.6
118/331 [ OK ] hdf5/1.12.0
119/331 [ OK ] hdf5/1.12.1
120/331 [ OK ] hdf5/1.12.2
121/331 [ OK ] hisat2/2.1.0
122/331 [ OK ] hisat2/2.2.0
123/331 [ OK ] htslib/1.9
124/331 [ OK ] htslib/1.10.2
125/331 [ OK ] htslib/1.11
126/331 [ OK ] htslib/1.13
127/331 [ OK ] htslib/1.14
128/331 [ OK ] htslib/1.15
129/331 [ OK ] htslib/1.15.1
130/331 [ OK ] htslib/1.16
131/331 [ OK ] htslib/1.17
132/331 [ OK ] htslib/1.18
133/331 [ OK ] htstools/0.1.1
134/331 [ OK ] igv/2.4.19
135/331 [ OK ] igv/2.7.0
136/331 [ OK ] igv/2.7.2
137/331 [ OK ] igv/2.8.2
138/331 [ OK ] igv/2.8.6
139/331 [ OK ] igv/2.8.13
140/331 [ OK ] igv/2.9.1
141/331 [ OK ] igv/2.11.0
142/331 [ OK ] igv/2.11.9
143/331 [ OK ] igv/2.12.3
144/331 [ OK ] igv/2.13.0
145/331 [ OK ] igv/2.14.0
146/331 [ OK ] igv/2.14.1
147/331 [ OK ] igv/2.15.1
148/331 [ OK ] igv/2.15.4
149/331 [ OK ] igv/2.16.0
150/331 [ OK ] igv/2.16.1
151/331 [ OK ] igv/2.16.2
152/331 [ OK ] igvtools/2.4.19
153/331 [ OK ] jags/4.3.0
154/331 [ OK ] jags/4.3.1
155/331 [ OK ] jq/1.5
156/331 [ OK ] jq/1.7
157/331 [ OK ] kallisto/0.45.0
158/331 [ OK ] kallisto/0.45.1
159/331 [ OK ] kallisto/0.46.0
160/331 [ OK ] kallisto/0.46.1
161/331 [ OK ] kallisto/0.46.2
162/331 [ OK ] kallisto/0.50.0
163/331 [ OK ] markdownlint-cli/0.32.2
164/331 [ OK ] markdownlint-cli/0.35.0
165/331 [ OK ] mc/4.8.30
166/331 [FAIL] miniconda3-py39/4.12.0: cannot load
167/331 [ OK ] miniconda3/4.12.0-py39
168/331 [ OK ] miniconda3/22.11.1-1-py310
169/331 [ OK ] miniconda3/23.3.1-0-py39
170/331 [ OK ] miniconda3/23.5.2-0-py39
171/331 [ OK ] miniconda3/23.5.2-0-py310
172/331 [ OK ] miniconda3/23.5.2-0-py311
173/331 [FAIL] mutect/1.1.1: cannot load
174/331 [FAIL] mutect/1.1.4: cannot load
175/331 [FAIL] mutect/1.1.5: cannot load
176/331 [ OK ] ncdu/2.2.1
177/331 [ OK ] pandoc/3.1.8
178/331 [ OK ] pdfcrop/0.4b
179/331 [ OK ] pdfcrop/1.42
180/331 [ OK ] picard/2.21.1
181/331 [ OK ] picard/2.21.4
182/331 [ OK ] picard/2.22.2
183/331 [ OK ] picard/2.23.1
184/331 [ OK ] picard/2.24.0
185/331 [ OK ] picard/2.26.2
188/331 [ OK ] picard/2.27.4
189/331 [ OK ] picard/2.27.5
190/331 [ OK ] pindel/0.2.5b8
191/331 [ OK ] plink/1.07
192/331 [ OK ] plink/1.90b6.10
196/331 [ OK ] plink/1.90b6.24
197/331 [ OK ] plink/1.90b6.25
198/331 [ OK ] plink/1.90b6.26
199/331 [ OK ] plink2/2.00a2LM
201/331 [ OK ] port4me/0.6.0
202/331 [ OK ] proj/4.9.3
203/331 [ OK ] qtop/0.9.20161222
204/331 [ OK ] quarto/1.3.433
205/331 [ OK ] quarto/1.3.450
206/331 [ OK ] r-siteconfig/0.3
207/331 [ OK ] rclone/1.63.0
208/331 [ OK ] rclone/1.63.1
209/331 [ OK ] rclone/1.64.0
291/331 [ OK ] tophat/2.1.1
292/331 [ OK ] tree/2.1.1
293/331 [ OK ] trimgalore/0.6.7
294/331 [ OK ] trimgalore/0.6.10
295/331 [ OK ] up/0.4
296/331 [ OK ] varscan/2.4.2
297/331 [ OK ] varscan/2.4.6
298/331 [ OK ] vcf-validator/0.9.2
299/331 [ OK ] vcf-validator/0.9.3
300/331 [ OK ] vcf-validator/0.9.4
301/331 [ OK ] vcf-validator/0.9.5
302/331 [ OK ] vcftools/0.1.16
303/331 [ OK ] wynton-tools/0.2.0
304/331 [ OK ] x86-64-level/0.2.2
306/331 [ OK ] yq/4.35.2
307/331 [ OK ] emacs/29.1
308/331 [ OK ] expect/5.45.4
309/331 [ OK ] htop/3.2.2
310/331 [ OK ] r/3.5.3
311/331 [ OK ] r/3.6.3
312/331 [ OK ] r/4.0.0-gcc10
313/331 [ OK ] r/4.0.0
314/331 [ OK ] r/4.0.5-gcc10
315/331 [ OK ] r/4.0.5
316/331 [ OK ] r/4.1.3-gcc8
317/331 [ OK ] r/4.1.3
318/331 [ OK ] r/4.2.0-gcc10
319/331 [ OK ] r/4.2.0
320/331 [ OK ] r/4.2.3-gcc10
321/331 [ OK ] r/4.2.3
322/331 [ OK ] r/4.3.0-gcc10

324/331 [ OK ] r/4.3.1-gcc10
325/331 [ OK ] r/4.3.1
326/331 [ OK ] scl-gcc-toolset/9
327/331 [ OK ] scl-gcc-toolset/10
328/331 [ OK ] scl-gcc-toolset/11
329/331 [ OK ] scl-gcc-toolset/12
330/331 [ OK ] sqlite/3.43.0
331/331 [ OK ] sqlite/3.43.2
   (from function `fail' in file /wynton/home/cbi/shared/software/CBI/bats-support-0.3.0/src/error.bash, line 40,
    from function `assert_lmod_repo' in file /wynton/home/cbi/hb/shared/repositories/wynton-tests/tests/incl/utils.sh, line 361,
    in test file /wynton/home/cbi/hb/shared/repositories/wynton-tests/tests/lmod-repo-CBI.bats, line 12)
     `assert_lmod_repo "CBI"' failed
   MODULE WARNING: bcftools 1.11 has a bug that results in valid but incorrect CIGAR strings. Because of this, it is recommended to use an older or a newer version instead. For details, see
   https://github.com/samtools/htslib/issues/1236
   MODULE WARNING: htslib 1.11 has a bug that results in valid but incorrect CIGAR strings. Because of this, it is recommended to use an older or a newer version instead. For details, see
   https://github.com/samtools/htslib/issues/1236
   Lmod has detected the following error: The CBI 'miniconda3-py39/4.12.0' module has been renamed to 'miniconda3/4.12.0-py39'; please use the latter instead
   While processing the following module(s):
       Module fullname         Module Filename
       ---------------         ---------------
       miniconda3-py39/4.12.0  /wynton/home/cbi/shared/modulefiles/CBI/miniconda3-py39/4.12.0.lua

   Note: the module "miniconda3-py39/4.12.0" cannot be unloaded because it was not loaded.

   Lmod Warning: mutect/1.1.1 requires Java v1.7, but you are running openjdk version "17.0.9" 2023-10-17 LTS
   While processing the following module(s):
       Module fullname  Module Filename
       ---------------  ---------------
       mutect/1.1.1     /wynton/home/cbi/shared/modulefiles/CBI/mutect/1.1.1.lua

   Lmod Warning: mutect/1.1.1 requires Java v1.7, but you are running openjdk version "17.0.9" 2023-10-17 LTS
   While processing the following module(s):
       Module fullname  Module Filename
       ---------------  ---------------
       mutect/1.1.1     /wynton/home/cbi/shared/modulefiles/CBI/mutect/1.1.1.lua

   Lmod Warning: mutect/1.1.1 requires Java v1.7, but you are running openjdk version "17.0.9" 2023-10-17 LTS
   While processing the following module(s):
       Module fullname  Module Filename
       ---------------  ---------------
       mutect/1.1.1     /wynton/home/cbi/shared/modulefiles/CBI/mutect/1.1.1.lua

   Lmod Warning: mutect/1.1.4 requires Java v1.7, but you are running openjdk version "17.0.9" 2023-10-17 LTS
   While processing the following module(s):
       Module fullname  Module Filename
       ---------------  ---------------
       mutect/1.1.4     /wynton/home/cbi/shared/modulefiles/CBI/mutect/1.1.4.lua

   Lmod Warning: mutect/1.1.4 requires Java v1.7, but you are running openjdk version "17.0.9" 2023-10-17 LTS
   While processing the following module(s):
       Module fullname  Module Filename
       ---------------  ---------------
       mutect/1.1.4     /wynton/home/cbi/shared/modulefiles/CBI/mutect/1.1.4.lua

   Lmod Warning: mutect/1.1.4 requires Java v1.7, but you are running openjdk version "17.0.9" 2023-10-17 LTS
   While processing the following module(s):
       Module fullname  Module Filename
       ---------------  ---------------
       mutect/1.1.4     /wynton/home/cbi/shared/modulefiles/CBI/mutect/1.1.4.lua

   Lmod Warning: mutect/1.1.5 requires Java v1.7, but you are running openjdk version "17.0.9" 2023-10-17 LTS
   While processing the following module(s):
       Module fullname  Module Filename
       ---------------  ---------------
       mutect/1.1.5     /wynton/home/cbi/shared/modulefiles/CBI/mutect/1.1.5.lua

   Lmod Warning: mutect/1.1.5 requires Java v1.7, but you are running openjdk version "17.0.9" 2023-10-17 LTS
   While processing the following module(s):
       Module fullname  Module Filename
       ---------------  ---------------
       mutect/1.1.5     /wynton/home/cbi/shared/modulefiles/CBI/mutect/1.1.5.lua

   Lmod Warning: mutect/1.1.5 requires Java v1.7, but you are running openjdk version "17.0.9" 2023-10-17 LTS
   While processing the following module(s):
       Module fullname  Module Filename
       ---------------  ---------------
       mutect/1.1.5     /wynton/home/cbi/shared/modulefiles/CBI/mutect/1.1.5.lua

   The following have been reloaded with a version change:
     1) openjdk/17 => openjdk/1.8.0

   MODULE WARNING: samtools 1.11 has a bug that results in valid but incorrect CIGAR strings. Because of this, it is recommended to use an older or a newer version instead. For details, see
   https://github.com/samtools/htslib/issues/1236
   Failed modules: [n=4] miniconda3-py39/4.12.0 mutect/1.1.1 mutect/1.1.4 mutect/1.1.5

1 test, 1 failure
HenrikBengtsson commented 7 months ago

All good now.