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feat: add cnvkit #1225

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feat: add cnvkit #1225

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khurrammaqbool
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This PR:

Fixed: cnvkit container.

Review and tests:

  • Tests pass
  • Code review
  • New code is executed and covered by tests, and test approve

@khurrammaqbool khurrammaqbool requested a review from a team August 14, 2023 13:26
@khurrammaqbool khurrammaqbool changed the base branch from master to develop August 14, 2023 13:29
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codecov bot commented Aug 14, 2023 •
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Codecov Report

Patch and project coverage have no change.

Comparison is base (f76d8a1) 99.42% compared to head (6f16e39) 99.42%.

❗ Current head 6f16e39 differs from pull request most recent head 2069abe. Consider uploading reports for the commit 2069abe to get more accurate results

Additional details and impacted files 
@@           Coverage Diff            @@
##           develop    #1225   +/-   ##
========================================
  Coverage    99.42%   99.42%           
========================================
  Files           41       41           
  Lines         1916     1916           
========================================
  Hits          1905     1905           
  Misses          11       11
Flag Coverage Δ
unittests 99.42% <ø> (ø)

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@khurrammaqbool
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Complete log from the failed build of cnvkit container is given below:

/usr/bin/docker buildx build --build-arg CONTAINER_NAME=varcall_cnvkit --file BALSAMIC/containers/varcall_cnvkit/Dockerfile --iidfile /tmp/docker-build-push-a8wlHq/iidfile --secret id=GIT_AUTH_TOKEN,src=/tmp/docker-build-push-a8wlHq/tmp-1775-5ulP00ZwmBK5 --tag clinicalgenomics/balsamic:add_cadd_container-varcall_cnvkit --metadata-file /tmp/docker-build-push-a8wlHq/metadata-file https://github.com/Clinical-Genomics/BALSAMIC.git#3bbf9b3560e5b3467ecc62f7108b4126132f9f75
#0 building with "default" instance using docker driver

#1 [internal] load git source https://github.com/Clinical-Genomics/BALSAMIC.git#3bbf9b3560e5b3467ecc62f7108b4126132f9f75
#1 0.063 Initialized empty Git repository in /var/lib/docker/overlay2/ownocybkpxu3wpe7rjmiuaxfv/diff/
#1 0.160 fatal: Not a valid object name 3bbf9b3560e5b3467ecc62f7108b4126132f9f75^{commit}
#1 6.147 From https://github.com/Clinical-Genomics/BALSAMIC
#1 6.147  * [new branch]        core_pipeline_restructuring -> origin/core_pipeline_restructuring
#1 6.147  * [new branch]        develop                 -> origin/develop
#1 6.147  * [new branch]        feat/add_cadd_container -> origin/feat/add_cadd_container
#1 6.147  * [new branch]        feat_map_per_lane       -> origin/feat_map_per_lane
#1 6.147  * [new branch]        fix-doc-urls            -> origin/fix-doc-urls
#1 6.148  * [new branch]        fix_cnvpytor_float      -> origin/fix_cnvpytor_float
#1 6.148  * [new branch]        git_action_build_containers -> origin/git_action_build_containers
#1 6.148  * [new branch]        master                  -> origin/master
#1 6.148  * [new branch]        update-action           -> origin/update-action
#1 6.149  * [new branch]        update-docker-actions   -> origin/update-docker-actions
#1 6.149  * [new branch]        updating_verification_report_template -> origin/updating_verification_report_template
#1 6.149  * [new branch]        url-actions             -> origin/url-actions
#1 6.149  * [new tag]           v12.0.2                 -> v12.0.2
#1 6.176  * [new tag]           1.1.0                   -> 1.1.0
#1 6.176  * [new tag]           1.9.0                   -> 1.9.0
#1 6.176  * [new tag]           2.6.1                   -> 2.6.1
#1 6.176  * [new tag]           2.9.0                   -> 2.9.0
#1 6.176  * [new tag]           3.0.1                   -> 3.0.1
#1 6.176  * [new tag]           v10.0.0                 -> v10.0.0
#1 6.176  * [new tag]           v10.0.1                 -> v10.0.1
#1 6.177  * [new tag]           v10.0.2                 -> v10.0.2
#1 6.177  * [new tag]           v10.0.3                 -> v10.0.3
#1 6.177  * [new tag]           v10.0.4                 -> v10.0.4
#1 6.177  * [new tag]           v10.0.5                 -> v10.0.5
#1 6.177  * [new tag]           v11.0.0                 -> v11.0.0
#1 6.177  * [new tag]           v11.0.1                 -> v11.0.1
#1 6.178  * [new tag]           v11.0.2                 -> v11.0.2
#1 6.178  * [new tag]           v11.1.0                 -> v11.1.0
#1 6.178  * [new tag]           v11.2.0                 -> v11.2.0
#1 6.178  * [new tag]           v12.0.0                 -> v12.0.0
#1 6.178  * [new tag]           v12.0.1                 -> v12.0.1
#1 6.178  * [new tag]           v2.9.6                  -> v2.9.6
#1 6.178  * [new tag]           v2.9.7                  -> v2.9.7
#1 6.178  * [new tag]           v2.9.8                  -> v2.9.8
#1 6.179  * [new tag]           v3.0.1                  -> v3.0.1
#1 6.179  * [new tag]           v3.1.1                  -> v3.1.1
#1 6.179  * [new tag]           v3.1.2                  -> v3.1.2
#1 6.179  * [new tag]           v3.1.3                  -> v3.1.3
#1 6.179  * [new tag]           v3.1.4                  -> v3.1.4
#1 6.179  * [new tag]           v3.2.0                  -> v3.2.0
#1 6.180  * [new tag]           v3.2.1                  -> v3.2.1
#1 6.180  * [new tag]           v3.2.2                  -> v3.2.2
#1 6.180  * [new tag]           v3.2.3                  -> v3.2.3
#1 6.180  * [new tag]           v3.3.0                  -> v3.3.0
#1 6.180  * [new tag]           v3.3.1                  -> v3.3.1
#1 6.180  * [new tag]           v4.0.0                  -> v4.0.0
#1 6.180  * [new tag]           v4.0.1                  -> v4.0.1
#1 6.180  * [new tag]           v4.1.0                  -> v4.1.0
#1 6.180  * [new tag]           v4.2.0                  -> v4.2.0
#1 6.180  * [new tag]           v4.2.1                  -> v4.2.1
#1 6.180  * [new tag]           v4.2.2                  -> v4.2.2
#1 6.180  * [new tag]           v4.2.3                  -> v4.2.3
#1 6.180  * [new tag]           v4.2.4                  -> v4.2.4
#1 6.180  * [new tag]           v4.3.0                  -> v4.3.0
#1 6.180  * [new tag]           v4.4.0                  -> v4.4.0
#1 6.180  * [new tag]           v4.5.0                  -> v4.5.0
#1 6.180  * [new tag]           v5.0.0                  -> v5.0.0
#1 6.181  * [new tag]           v5.0.1                  -> v5.0.1
#1 6.181  * [new tag]           v5.1.0                  -> v5.1.0
#1 6.181  * [new tag]           v6.0.0                  -> v6.0.0
#1 6.181  * [new tag]           v6.0.1                  -> v6.0.1
#1 6.181  * [new tag]           v6.0.2                  -> v6.0.2
#1 6.181  * [new tag]           v6.0.3                  -> v6.0.3
#1 6.181  * [new tag]           v6.0.4                  -> v6.0.4
#1 6.181  * [new tag]           v6.1.0                  -> v6.1.0
#1 6.181  * [new tag]           v6.1.1                  -> v6.1.1
#1 6.181  * [new tag]           v6.1.2                  -> v6.1.2
#1 6.181  * [new tag]           v7.0.0                  -> v7.0.0
#1 6.181  * [new tag]           v7.0.1                  -> v7.0.1
#1 6.181  * [new tag]           v7.0.2                  -> v7.0.2
#1 6.181  * [new tag]           v7.1.0                  -> v7.1.0
#1 6.181  * [new tag]           v7.1.1                  -> v7.1.1
#1 6.181  * [new tag]           v7.1.10                 -> v7.1.10
#1 6.181  * [new tag]           v7.1.2                  -> v7.1.2
#1 6.182  * [new tag]           v7.1.3                  -> v7.1.3
#1 6.182  * [new tag]           v7.1.4                  -> v7.1.4
#1 6.182  * [new tag]           v7.1.5                  -> v7.1.5
#1 6.182  * [new tag]           v7.1.6                  -> v7.1.6
#1 6.182  * [new tag]           v7.1.7                  -> v7.1.7
#1 6.182  * [new tag]           v7.1.8                  -> v7.1.8
#1 6.182  * [new tag]           v7.1.9                  -> v7.1.9
#1 6.182  * [new tag]           v7.2.0                  -> v7.2.0
#1 6.182  * [new tag]           v7.2.1                  -> v7.2.1
#1 6.182  * [new tag]           v7.2.2                  -> v7.2.2
#1 6.182  * [new tag]           v7.2.3                  -> v7.2.3
#1 6.182  * [new tag]           v7.2.4                  -> v7.2.4
#1 6.182  * [new tag]           v7.2.5                  -> v7.2.5
#1 6.182  * [new tag]           v7.2.6                  -> v7.2.6
#1 6.182  * [new tag]           v8.0.0                  -> v8.0.0
#1 6.183  * [new tag]           v8.0.1                  -> v8.0.1
#1 6.183  * [new tag]           v8.0.2                  -> v8.0.2
#1 6.183  * [new tag]           v8.1.0                  -> v8.1.0
#1 6.183  * [new tag]           v8.2.0                  -> v8.2.0
#1 6.183  * [new tag]           v8.2.1                  -> v8.2.1
#1 6.183  * [new tag]           v8.2.10                 -> v8.2.10
#1 6.183  * [new tag]           v8.2.2                  -> v8.2.2
#1 6.183  * [new tag]           v8.2.3                  -> v8.2.3
#1 6.183  * [new tag]           v8.2.4                  -> v8.2.4
#1 6.183  * [new tag]           v8.2.5                  -> v8.2.5
#1 6.183  * [new tag]           v8.2.6                  -> v8.2.6
#1 6.183  * [new tag]           v8.2.7                  -> v8.2.7
#1 6.183  * [new tag]           v8.2.8                  -> v8.2.8
#1 6.183  * [new tag]           v8.2.9                  -> v8.2.9
#1 6.183  * [new tag]           v9.0.0                  -> v9.0.0
#1 6.183  * [new tag]           v9.0.1                  -> v9.0.1
#1 DONE 7.3s

#2 [auth] continuumio/miniconda3:pull token for registry-1.docker.io
#2 DONE 0.0s

#3 [internal] load metadata for docker.io/continuumio/miniconda3:4.10.3-alpine
#3 DONE 0.4s

#4 [1/5] FROM docker.io/continuumio/miniconda3:4.10.3-alpine@sha256:e007b47bbf7de9db9adec13588593d02cdaf0c32ee257f7a2f88737bf8b9945d
#4 resolve docker.io/continuumio/miniconda3:4.10.3-alpine@sha256:e007b47bbf7de9db9adec13588593d02cdaf0c32ee257f7a2f88737bf8b9945d 0.0s done
#4 extracting sha256:5843afab387455b37944e709ee8c78d7520df80f8d01cf7f861aae63beeddb6b 0.1s
#4 sha256:87d798ddb41cc74065ceeda1bb7b59a10e76c7d70b02c411d6015c6fb3f3673f 9.44MB / 58.90MB 0.2s
#4 sha256:e007b47bbf7de9db9adec13588593d02cdaf0c32ee257f7a2f88737bf8b9945d 951B / 951B done
#4 sha256:8afb5f84671e5f45e16fa858da086a45fb1bf12aafd9beba4e8bd946d4e65ebd 5.80kB / 5.80kB done
#4 sha256:5843afab387455b37944e709ee8c78d7520df80f8d01cf7f861aae63beeddb6b 2.81MB / 2.81MB 0.1s done
#4 sha256:72c585c386a3645e6a1ad80518aafc474e0534ae582272c2c86834c434a36dbe 5.24MB / 5.75MB 0.2s
#4 sha256:87d798ddb41cc74065ceeda1bb7b59a10e76c7d70b02c411d6015c6fb3f3673f 25.17MB / 58.90MB 0.3s
#4 sha256:72c585c386a3645e6a1ad80518aafc474e0534ae582272c2c86834c434a36dbe 5.75MB / 5.75MB 0.2s done
#4 sha256:87d798ddb41cc74065ceeda1bb7b59a10e76c7d70b02c411d6015c6fb3f3673f 40.89MB / 58.90MB 0.4s
#4 extracting sha256:5843afab387455b37944e709ee8c78d7520df80f8d01cf7f861aae63beeddb6b 0.4s done
#4 sha256:87d798ddb41cc74065ceeda1bb7b59a10e76c7d70b02c411d6015c6fb3f3673f 57.08MB / 58.90MB 0.5s
#4 sha256:87d798ddb41cc74065ceeda1bb7b59a10e76c7d70b02c411d6015c6fb3f3673f 58.90MB / 58.90MB 0.6s done
#4 extracting sha256:72c585c386a3645e6a1ad80518aafc474e0534ae582272c2c86834c434a36dbe
#4 extracting sha256:72c585c386a3645e6a1ad80518aafc474e0534ae582272c2c86834c434a36dbe 0.2s done
#4 extracting sha256:87d798ddb41cc74065ceeda1bb7b59a10e76c7d70b02c411d6015c6fb3f3673f 0.1s
#4 extracting sha256:87d798ddb41cc74065ceeda1bb7b59a10e76c7d70b02c411d6015c6fb3f3673f 2.4s done
#4 DONE 6.0s

#5 [2/5] RUN apk add --no-cache bash gcc git zlib-dev musl-dev
#5 0.227 fetch https://dl-cdn.alpinelinux.org/alpine/v3.14/main/x86_64/APKINDEX.tar.gz
#5 0.320 fetch https://dl-cdn.alpinelinux.org/alpine/v3.14/community/x86_64/APKINDEX.tar.gz
#5 0.512 (1/22) Upgrading musl (1.2.2-r3 -> 1.2.2-r5)
#5 0.527 (2/22) Upgrading zlib (1.2.11-r3 -> 1.2.12-r3)
#5 0.536 (3/22) Installing libstdc++ (10.3.1_git20210424-r2)
#5 0.603 (4/22) Installing binutils (2.35.2-r2)
#5 0.684 (5/22) Installing libgomp (10.3.1_git20210424-r2)
#5 0.711 (6/22) Installing libatomic (10.3.1_git20210424-r2)
#5 0.723 (7/22) Installing libgphobos (10.3.1_git20210424-r2)
#5 0.782 (8/22) Installing gmp (6.2.1-r1)
#5 0.794 (9/22) Installing isl22 (0.22-r0)
#5 0.817 (10/22) Installing mpfr4 (4.1.0-r0)
#5 0.849 (11/22) Installing mpc1 (1.2.1-r0)
#5 0.857 (12/22) Installing gcc (10.3.1_git20210424-r2)
#5 1.650 (13/22) Installing ca-certificates (20230506-r0)
#5 1.669 (14/22) Installing brotli-libs (1.0.9-r5)
#5 1.683 (15/22) Installing nghttp2-libs (1.43.0-r0)
#5 1.691 (16/22) Installing libcurl (8.0.1-r0)
#5 1.704 (17/22) Installing expat (2.5.0-r0)
#5 1.712 (18/22) Installing pcre2 (10.36-r1)
#5 1.726 (19/22) Installing git (2.32.7-r0)
#5 1.862 (20/22) Installing musl-dev (1.2.2-r5)
#5 1.947 (21/22) Installing pkgconf (1.7.4-r1)
#5 1.956 (22/22) Installing zlib-dev (1.2.12-r3)
#5 1.965 Executing busybox-1.33.1-r2.trigger
#5 1.969 Executing ca-certificates-20230506-r0.trigger
#5 1.997 Executing glibc-bin-2.33-r0.trigger
#5 2.000 /usr/glibc-compat/sbin/ldconfig: /usr/glibc-compat/lib/ld-linux-x86-64.so.2 is not a symbolic link
#5 2.000 
#5 2.008 OK: 155 MiB in 44 packages
#5 DONE 2.5s

#6 [3/5] COPY . /project
#6 DONE 1.0s

#7 [4/5] RUN cd /project/BALSAMIC/containers/varcall_cnvkit/ && /bin/sh varcall_cnvkit.sh varcall_cnvkit
#7 0.611 Collecting package metadata (repodata.json): ...working... done
#7 78.28 Solving environment: ...working... done
#7 290.6 
#7 290.6 
#7 290.6 ==> WARNING: A newer version of conda exists. <==
#7 290.6   current version: 4.10.3
#7 290.6   latest version: 23.7.2
#7 290.6 
#7 290.6 Please update conda by running
#7 290.6 
#7 290.6     $ conda update -n base -c defaults conda
#7 290.6 
#7 290.6 
#7 290.7 
#7 290.7 Downloading and Extracting Packages
#7 290.7 
readline-8.1.2       | 269 KB    |            |   0% 
readline-8.1.2       | 269 KB    | ########## | 100% 
#7 290.8 
gcc_impl_linux-64-10 | 46.7 MB   |            |   0% 
gcc_impl_linux-64-10 | 46.7 MB   | ##3        |  23% 
gcc_impl_linux-64-10 | 46.7 MB   | #####8     |  58% 
gcc_impl_linux-64-10 | 46.7 MB   | #########3 |  94% 
gcc_impl_linux-64-10 | 46.7 MB   | ########## | 100% 
#7 298.0 
gsl-2.7              | 3.2 MB    |            |   0% 
gsl-2.7              | 3.2 MB    | ########## | 100% 
gsl-2.7              | 3.2 MB    | ########## | 100% 
#7 298.7 
gxx_linux-64-10.4.0  | 27 KB     |            |   0% 
gxx_linux-64-10.4.0  | 27 KB     | ########## | 100% 
#7 298.7 
freetype-2.12.1      | 611 KB    |            |   0% 
freetype-2.12.1      | 611 KB    | ########## | 100% 
#7 298.8 
font-ttf-dejavu-sans | 388 KB    |            |   0% 
font-ttf-dejavu-sans | 388 KB    | ########## | 100% 
#7 298.9 
xorg-libxdmcp-1.1.3  | 19 KB     |            |   0% 
xorg-libxdmcp-1.1.3  | 19 KB     | ########## | 100% 
#7 298.9 
r-pillar-1.9.0       | 602 KB    |            |   0% 
r-pillar-1.9.0       | 602 KB    | ########## | 100% 
#7 298.9 
r-mclust-6.0.0       | 4.0 MB    |            |   0% 
r-mclust-6.0.0       | 4.0 MB    | ########## | 100% 
r-mclust-6.0.0       | 4.0 MB    | ########## | 100% 
#7 299.4 
bioconductor-matrixg | 342 KB    |            |   0% 
bioconductor-matrixg | 342 KB    | ########## | 100% 
#7 299.5 
ca-certificates-2023 | 145 KB    |            |   0% 
ca-certificates-2023 | 145 KB    | ########## | 100% 
#7 299.6 
r-cpp11-0.4.3        | 254 KB    |            |   0% 
r-cpp11-0.4.3        | 254 KB    | ########## | 100% 
#7 299.7 
libedit-3.1.20191231 | 121 KB    |            |   0% 
libedit-3.1.20191231 | 121 KB    | ########## | 100% 
#7 299.7 
ld_impl_linux-64-2.3 | 675 KB    |            |   0% 
ld_impl_linux-64-2.3 | 675 KB    | ########## | 100% 
#7 299.8 
jpeg-9e              | 235 KB    |            |   0% 
jpeg-9e              | 235 KB    | ########## | 100% 
#7 299.8 
libstdcxx-ng-13.1.0  | 3.7 MB    |            |   0% 
libstdcxx-ng-13.1.0  | 3.7 MB    | ########## | 100% 
libstdcxx-ng-13.1.0  | 3.7 MB    | ########## | 100% 
#7 299.9 
xz-5.2.5             | 343 KB    |            |   0% 
xz-5.2.5             | 343 KB    | ########## | 100% 
#7 300.0 
conda-package-handli | 247 KB    |            |   0% 
conda-package-handli | 247 KB    | ########## | 100% 
#7 300.1 
r-getopt-1.20.3      | 47 KB     |            |   0% 
r-getopt-1.20.3      | 47 KB     | ########## | 100% 
#7 300.1 
r-ellipsis-0.3.2     | 42 KB     |            |   0% 
r-ellipsis-0.3.2     | 42 KB     | ########## | 100% 
#7 300.1 
bioconductor-summari | 2.7 MB    |            |   0% 
bioconductor-summari | 2.7 MB    | ########## | 100% 
bioconductor-summari | 2.7 MB    | ########## | 100% 
#7 300.5 
keyutils-1.6.1       | [115](https://github.com/Clinical-Genomics/BALSAMIC/actions/runs/5855846314/job/15874424925?pr=1222#step:5:119) KB    |            |   0% 
keyutils-1.6.1       | 115 KB    | ########## | 100% 
#7 300.6 
r-rlang-1.0.5        | 1.5 MB    |            |   0% 
r-rlang-1.0.5        | 1.5 MB    | ########## | 100% 
r-rlang-1.0.5        | 1.5 MB    | ########## | 100% 
#7 300.8 
bioconductor-biocgen | 631 KB    |            |   0% 
bioconductor-biocgen | 631 KB    | ########## | 100% 
bioconductor-biocgen | 631 KB    | ########## | 100% 
#7 300.9 
bioconductor-rhdf5li | 3.8 MB    |            |   0% 
bioconductor-rhdf5li | 3.8 MB    | ########## | 100% 
bioconductor-rhdf5li | 3.8 MB    | ########## | 100% 
#7 301.7 
r-jsonlite-1.8.5     | 620 KB    |            |   0% 
r-jsonlite-1.8.5     | 620 KB    | ########## | 100% 
#7 301.7 
r-bit64-4.0.5        | 508 KB    |            |   0% 
r-bit64-4.0.5        | 508 KB    | ########## | 100% 
#7 301.8 
r-purrr-0.3.5        | 414 KB    |            |   0% 
r-purrr-0.3.5        | 414 KB    | ########## | 100% 
#7 301.9 
libcblas-3.9.0       | 14 KB     |            |   0% 
libcblas-3.9.0       | 14 KB     | ########## | 100% 
#7 302.0 
bioconductor-zlibbio | 115 KB    |            |   0% 
bioconductor-zlibbio | 115 KB    | ########## | 100% 
#7 302.0 
r-withr-2.5.0        | 240 KB    |            |   0% 
r-withr-2.5.0        | 240 KB    | ########## | 100% 
#7 302.1 
bioconductor-genomic | 2.2 MB    |            |   0% 
bioconductor-genomic | 2.2 MB    | ########## | 100% 
bioconductor-genomic | 2.2 MB    | ########## | 100% 
#7 302.4 
six-1.16.0           | 14 KB     |            |   0% 
six-1.16.0           | 14 KB     | ########## | 100% 
#7 302.4 
pip-23.2.1           | 1.3 MB    |            |   0% 
pip-23.2.1           | 1.3 MB    | ########## | 100% 
pip-23.2.1           | 1.3 MB    | ########## | 100% 
#7 302.5 
r-xml2-1.3.3         | 323 KB    |            |   0% 
r-xml2-1.3.3         | 323 KB    | ########## | 100% 
#7 302.6 
certifi-2023.5.7     | 149 KB    |            |   0% 
certifi-2023.5.7     | 149 KB    | ########## | 100% 
#7 302.7 
libopenblas-0.3.23   | 5.2 MB    |            |   0% 
libopenblas-0.3.23   | 5.2 MB    | ########## | 100% 
libopenblas-0.3.23   | 5.2 MB    | ########## | 100% 
#7 302.9 
r-rappdirs-0.3.3     | 52 KB     |            |   0% 
r-rappdirs-0.3.3     | 52 KB     | ########## | 100% 
#7 302.9 
xorg-libxt-1.3.0     | 371 KB    |            |   0% 
xorg-libxt-1.3.0     | 371 KB    | ########## | 100% 
#7 303.0 
r-colorspace-2.1_0   | 2.4 MB    |            |   0% 
r-colorspace-2.1_0   | 2.4 MB    | ########## | 100% 
#7 303.0 
r-munsell-0.5.0      | 248 KB    |            |   0% 
r-munsell-0.5.0      | 248 KB    | ########## | 100% 
#7 303.1 
r-gridextra-2.3      | 1.1 MB    |            |   0% 
r-gridextra-2.3      | 1.1 MB    | ########## | 100% 
r-gridextra-2.3      | 1.1 MB    | ########## | 100% 
#7 303.3 
r-restfulr-0.0.15    | 388 KB    |            |   0% 
r-restfulr-0.0.15    | 388 KB    | ########## | 100% 
r-restfulr-0.0.15    | 388 KB    | ########## | 100% 
#7 303.4 
r-r6-2.5.1           | 90 KB     |            |   0% 
r-r6-2.5.1           | 90 KB     | ########## | 100% 
#7 303.4 
r-snow-0.4_4         | 114 KB    |            |   0% 
r-snow-0.4_4         | 114 KB    | ########## | 100% 
#7 303.5 
bioconductor-genomic | 2.2 MB    |            |   0% 
bioconductor-genomic | 2.2 MB    | ########## | 100% 
bioconductor-genomic | 2.2 MB    | ########## | 100% 
#7 303.8 
r-matrixstats-1.0.0  | 455 KB    |            |   0% 
r-matrixstats-1.0.0  | 455 KB    | ########## | 100% 
#7 303.9 
packaging-23.1       | 45 KB     |            |   0% 
packaging-23.1       | 45 KB     | ########## | 100% 
#7 303.9 
r-curl-4.3.3         | 699 KB    |            |   0% 
r-curl-4.3.3         | 699 KB    | ########## | 100% 
r-curl-4.3.3         | 699 KB    | ########## | 100% 
#7 304.0 
harfbuzz-6.0.0       | 1.2 MB    |            |   0% 
harfbuzz-6.0.0       | 1.2 MB    | ########## | 100% 
#7 304.1 
r-rcolorbrewer-1.1_3 | 65 KB     |            |   0% 
r-rcolorbrewer-1.1_3 | 65 KB     | ########## | 100% 
#7 304.2 
r-nlme-3.1_162       | 2.2 MB    |            |   0% 
r-nlme-3.1_162       | 2.2 MB    | ########## | 100% 
#7 304.2 
ruamel.yaml.clib-0.2 | 143 KB    |            |   0% 
ruamel.yaml.clib-0.2 | 143 KB    | ########## | 100% 
#7 304.3 
r-dplyr-1.1.2        | 1.3 MB    |            |   0% 
r-dplyr-1.1.2        | 1.3 MB    | ########## | 100% 
#7 304.3 
font-ttf-inconsolata | 94 KB     |            |   0% 
font-ttf-inconsolata | 94 KB     | ########## | 100% 
#7 304.4 
r-pkgconfig-2.0.3    | 26 KB     |            |   0% 
r-pkgconfig-2.0.3    | 26 KB     | ########## | 100% 
#7 304.4 
libtiff-4.4.0        | 642 KB    |            |   0% 
libtiff-4.4.0        | 642 KB    | ########## | 100% 
libtiff-4.4.0        | 642 KB    | ########## | 100% 
#7 304.6 
r-rcpp-1.0.10        | 1.9 MB    |            |   0% 
r-rcpp-1.0.10        | 1.9 MB    | ########## | 100% 
r-rcpp-1.0.10        | 1.9 MB    | ########## | 100% 
#7 304.8 
r-generics-0.1.3     | 92 KB     |            |   0% 
r-generics-0.1.3     | 92 KB     | ########## | 100% 
r-generics-0.1.3     | 92 KB     | ########## | 100% 
#7 305.0 
tktable-2.10         | 89 KB     |            |   0% 
tktable-2.10         | 89 KB     | ########## | 100% 
#7 305.1 
bioconductor-s4vecto | 2.2 MB    |            |   0% 
bioconductor-s4vecto | 2.2 MB    | ########## | 100% 
bioconductor-s4vecto | 2.2 MB    | ########## | 100% 
#7 305.4 
tabix-1.11           | 6 KB      |            |   0% 
tabix-1.11           | 6 KB      | ########## | 100% 
#7 305.4 
bioconductor-biocio- | 419 KB    |            |   0% 
bioconductor-biocio- | 419 KB    | ########## | 100% 
#7 305.5 
pcre2-10.37          | 1.1 MB    |            |   0% 
pcre2-10.37          | 1.1 MB    | ########## | 100% 
pcre2-10.37          | 1.1 MB    | ########## | 100% 
#7 305.7 
bioconductor-rhdf5fi | 646 KB    |            |   0% 
bioconductor-rhdf5fi | 646 KB    | ########## | 100% 
bioconductor-rhdf5fi | 646 KB    | ########## | 100% 
#7 305.9 
font-ttf-ubuntu-0.83 | 1.9 MB    |            |   0% 
font-ttf-ubuntu-0.83 | 1.9 MB    | ########## | 100% 
font-ttf-ubuntu-0.83 | 1.9 MB    | ########## | 100% 
#7 306.2 
r-lambda.r-1.2.4     | 121 KB    |            |   0% 
r-lambda.r-1.2.4     | 121 KB    | ########## | 100% 
#7 306.2 
bioconductor-genomei | 8 KB      |            |   0% 
bioconductor-genomei | 8 KB      | ########## | 100% 
#7 306.2 
r-openssl-2.0.5      | 621 KB    |            |   0% 
r-openssl-2.0.5      | 621 KB    | ########## | 100% 
#7 306.3 
tk-8.6.12            | 3.3 MB    |            |   0% 
tk-8.6.12            | 3.3 MB    | ########## | 100% 
tk-8.6.12            | 3.3 MB    | ########## | 100% 
#7 306.9 
r-hms-1.1.3          | 104 KB    |            |   0% 
r-hms-1.1.3          | 104 KB    | ########## | 100% 
#7 306.9 
binutils_impl_linux- | 4.7 MB    |            |   0% 
binutils_impl_linux- | 4.7 MB    | ########## | 100% 
binutils_impl_linux- | 4.7 MB    | ########## | 100% 
#7 307.1 
libgfortran-ng-13.1. | 23 KB     |            |   0% 
libgfortran-ng-13.1. | 23 KB     | ########## | 100% 
#7 307.1 
libpng-1.6.39        | 276 KB    |            |   0% 
libpng-1.6.39        | 276 KB    | ########## | 100% 
#7 307.2 
conda-23.5.2         | 994 KB    |            |   0% 
conda-23.5.2         | 994 KB    | ########## | 100% 
conda-23.5.2         | 994 KB    | ########## | 100% 
#7 307.3 
zstd-1.5.2           | 421 KB    |            |   0% 
zstd-1.5.2           | 421 KB    | ########## | 100% 
#7 307.3 
fontconfig-2.14.2    | 266 KB    |            |   0% 
fontconfig-2.14.2    | 266 KB    | ########## | 100% 
#7 307.4 
r-assertthat-0.2.1   | 71 KB     |            |   0% 
r-assertthat-0.2.1   | 71 KB     | ########## | 100% 
#7 307.4 
r-futile.options-1.0 | 28 KB     |            |   0% 
r-futile.options-1.0 | 28 KB     | ########## | 100% 
#7 307.5 
libxml2-2.9.14       | 771 KB    |            |   0% 
libxml2-2.9.14       | 771 KB    | ########## | 100% 
libxml2-2.9.14       | 771 KB    | ########## | 100% 
#7 307.6 
zlib-1.2.13          | 91 KB     |            |   0% 
zlib-1.2.13          | 91 KB     | ########## | 100% 
#7 307.7 
zstandard-0.19.0     | 384 KB    |            |   0% 
zstandard-0.19.0     | 384 KB    | ########## | 100% 
#7 307.7 
expat-2.5.0          | 134 KB    |            |   0% 
expat-2.5.0          | 134 KB    | ########## | 100% 
#7 307.7 
gfortran_linux-64-10 | 28 KB     |            |   0% 
gfortran_linux-64-10 | 28 KB     | ########## | 100% 
#7 307.8 
bioconductor-rtrackl | 5.3 MB    |            |   0% 
bioconductor-rtrackl | 5.3 MB    | ########## | 100% 
bioconductor-rtrackl | 5.3 MB    | ########## | 100% 
#7 308.4 
gxx_impl_linux-64-10 | 11.5 MB   |            |   0% 
gxx_impl_linux-64-10 | 11.5 MB   | ######9    |  70% 
gxx_impl_linux-64-10 | 11.5 MB   | ########## | 100% 
#7 310.2 
libstdcxx-devel_linu | 9.6 MB    |            |   0% 
libstdcxx-devel_linu | 9.6 MB    | ########## | 100% 
libstdcxx-devel_linu | 9.6 MB    | ########## | 100% 
#7 311.8 
icu-70.1             | 13.5 MB   |            |   0% 
icu-70.1             | 13.5 MB   | ########4  |  85% 
icu-70.1             | 13.5 MB   | ########## | 100% 
#7 313.8 
libsanitizer-10.4.0  | 6.0 MB    |            |   0% 
libsanitizer-10.4.0  | 6.0 MB    | ########## | 100% 
libsanitizer-10.4.0  | 6.0 MB    | ########## | 100% 
#7 314.7 
pycparser-2.20       | 94 KB     |            |   0% 
pycparser-2.20       | 94 KB     | ########## | 100% 
#7 314.8 
cryptography-39.0.0  | 1.4 MB    |            |   0% 
cryptography-39.0.0  | 1.4 MB    | ########## | 100% 
#7 314.8 
bioconductor-rsamtoo | 3.8 MB    |            |   0% 
bioconductor-rsamtoo | 3.8 MB    | ########## | 100% 
bioconductor-rsamtoo | 3.8 MB    | ########## | 100% 
#7 315.3 
r-plogr-0.2.0        | 21 KB     |            |   0% 
r-plogr-0.2.0        | 21 KB     | ########## | 100% 
#7 315.4 
r-rcurl-1.98_1.12    | 797 KB    |            |   0% 
r-rcurl-1.98_1.12    | 797 KB    | ########## | 100% 
#7 315.4 
libnsl-2.0.0         | 31 KB     |            |   0% 
libnsl-2.0.0         | 31 KB     | ########## | 100% 
#7 315.5 
python_abi-3.8       | 6 KB      |            |   0% 
python_abi-3.8       | 6 KB      | ########## | 100% 
#7 315.5 
bioconductor-delayed | 2.4 MB    |            |   0% 
bioconductor-delayed | 2.4 MB    | ########## | 100% 
bioconductor-delayed | 2.4 MB    | ########## | 100% 
#7 315.8 
libev-4.33           | 104 KB    |            |   0% 
libev-4.33           | 104 KB    | ########## | 100% 
#7 315.9 
r-ggplot2-3.4.0      | 4.1 MB    |            |   0% 
r-ggplot2-3.4.0      | 4.1 MB    | ########## | 100% 
r-ggplot2-3.4.0      | 4.1 MB    | ########## | 100% 
#7 316.4 
r-mass-7.3_58.3      | 1.1 MB    |            |   0% 
r-mass-7.3_58.3      | 1.1 MB    | ########## | 100% 
#7 316.4 
fonts-conda-ecosyste | 4 KB      |            |   0% 
fonts-conda-ecosyste | 4 KB      | ########## | 100% 
#7 316.5 
r-base-4.1.3         | 24.5 MB   |            |   0% 
r-base-4.1.3         | 24.5 MB   | ###8       |  38% 
r-base-4.1.3         | 24.5 MB   | ########## | 100% 
r-base-4.1.3         | 24.5 MB   | ########## | 100% 
#7 319.5 
urllib3-1.26.6       | 99 KB     |            |   0% 
urllib3-1.26.6       | 99 KB     | ########## | 100% 
#7 319.6 
sed-4.8              | 264 KB    |            |   0% 
sed-4.8              | 264 KB    | ########## | 100% 
#7 319.7 
xorg-xproto-7.0.31   | 73 KB     |            |   0% 
xorg-xproto-7.0.31   | 73 KB     | ########## | 100% 
#7 319.7 
r-bit-4.0.5          | 1.1 MB    |            |   0% 
r-bit-4.0.5          | 1.1 MB    | ########## | 100% 
r-bit-4.0.5          | 1.1 MB    | ########## | 100% 
#7 319.9 
r-farver-2.1.1       | 1.4 MB    |            |   0% 
r-farver-2.1.1       | 1.4 MB    | ########## | 100% 
r-farver-2.1.1       | 1.4 MB    | ########## | 100% 
#7 320.1 
r-glue-1.6.2         | 155 KB    |            |   0% 
r-glue-1.6.2         | 155 KB    | ########## | 100% 
#7 320.1 
r-gtable-0.3.3       | 217 KB    |            |   0% 
r-gtable-0.3.3       | 217 KB    | ########## | 100% 
#7 320.2 
pthread-stubs-0.4    | 5 KB      |            |   0% 
pthread-stubs-0.4    | 5 KB      | ########## | 100% 
#7 320.2 
r-viridislite-0.4.1  | 1.3 MB    |            |   0% 
r-viridislite-0.4.1  | 1.3 MB    | ########## | 100% 
r-viridislite-0.4.1  | 1.3 MB    | ########## | 100% 
#7 320.4 
xorg-libsm-1.2.3     | 26 KB     |            |   0% 
xorg-libsm-1.2.3     | 26 KB     | ########## | 100% 
#7 320.4 
libgfortran5-13.1.0  | 1.4 MB    |            |   0% 
libgfortran5-13.1.0  | 1.4 MB    | ########## | 100% 
#7 320.5 
r-lattice-0.21_8     | 1.3 MB    |            |   0% 
r-lattice-0.21_8     | 1.3 MB    | ########## | 100% 
#7 320.5 
libblas-3.9.0        | 14 KB     |            |   0% 
libblas-3.9.0        | 14 KB     | ########## | 100% 
#7 320.5 
sqlite-3.36.0        | 1.4 MB    |            |   0% 
sqlite-3.36.0        | 1.4 MB    | ########## | 100% 
sqlite-3.36.0        | 1.4 MB    | ########## | 100% 
#7 320.8 
libcurl-7.86.0       | 348 KB    |            |   0% 
libcurl-7.86.0       | 348 KB    | ########## | 100% 
#7 320.9 
bioconductor-xvector | 731 KB    |            |   0% 
bioconductor-xvector | 731 KB    | ########## | 100% 
bioconductor-xvector | 731 KB    | ########## | 100% 
#7 321.0 
bcftools-1.15.1      | 863 KB    |            |   0% 
bcftools-1.15.1      | 863 KB    | ########## | 100% 
bcftools-1.15.1      | 863 KB    | ########## | 100% 
#7 321.2 
bioconductor-genomic | 2.3 MB    |            |   0% 
bioconductor-genomic | 2.3 MB    | ########## | 100% 
bioconductor-genomic | 2.3 MB    | ########## | 100% 
#7 321.5 
r-memoise-2.0.1      | 57 KB     |            |   0% 
r-memoise-2.0.1      | 57 KB     | ########## | 100% 
#7 321.6 
curl-7.86.0          | 91 KB     |            |   0% 
curl-7.86.0          | 91 KB     | ########## | 100% 
#7 321.6 
r-fastmap-1.1.1      | 68 KB     |            |   0% 
r-fastmap-1.1.1      | 68 KB     | ########## | 100% 
#7 321.6 
xorg-libice-1.0.10   | 58 KB     |            |   0% 
xorg-libice-1.0.10   | 58 KB     | ########## | 100% 
#7 321.7 
r-isoband-0.2.7      | 1.5 MB    |            |   0% 
r-isoband-0.2.7      | 1.5 MB    | ########## | 100% 
#7 321.7 
bioconductor-biocfil | 566 KB    |            |   0% 
bioconductor-biocfil | 566 KB    | ########## | 100% 
bioconductor-biocfil | 566 KB    | ########## | 100% 
#7 321.9 
r-fansi-1.0.4        | 308 KB    |            |   0% 
r-fansi-1.0.4        | 308 KB    | ########## | 100% 
#7 321.9 
libgcc-ng-13.1.0     | 758 KB    |            |   0% 
libgcc-ng-13.1.0     | 758 KB    | ########## | 100% 
#7 322.0 
chardet-4.0.0        | 205 KB    |            |   0% 
chardet-4.0.0        | 205 KB    | ########## | 100% 
#7 322.1 
r-cachem-1.0.8       | 73 KB     |            |   0% 
r-cachem-1.0.8       | 73 KB     | ########## | 100% 
#7 322.1 
binutils_linux-64-2. | 27 KB     |            |   0% 
binutils_linux-64-2. | 27 KB     | ########## | 100% 
#7 322.1 
yaml-0.2.5           | 87 KB     |            |   0% 
yaml-0.2.5           | 87 KB     | ########## | 100% 
#7 322.2 
bioconductor-variant | 3.6 MB    |            |   0% 
bioconductor-variant | 3.6 MB    | ########## | 100% 
bioconductor-variant | 3.6 MB    | ########## | 100% 
#7 322.6 
pango-1.50.14        | 427 KB    |            |   0% 
pango-1.50.14        | 427 KB    | ########## | 100% 
#7 322.7 
r-rjson-0.2.21       | 162 KB    |            |   0% 
r-rjson-0.2.21       | 162 KB    | ########## | 100% 
#7 322.8 
requests-2.25.1      | 51 KB     |            |   0% 
requests-2.25.1      | 51 KB     | ########## | 100% 
#7 322.8 
liblapack-3.9.0      | 14 KB     |            |   0% 
liblapack-3.9.0      | 14 KB     | ########## | 100% 
#7 322.8 
r-mgcv-1.8_42        | 3.1 MB    |            |   0% 
r-mgcv-1.8_42        | 3.1 MB    | ########## | 100% 
#7 322.9 
_libgcc_mutex-0.1    | 3 KB      |            |   0% 
_libgcc_mutex-0.1    | 3 KB      | ########## | 100% 
#7 322.9 
make-4.3             | 507 KB    |            |   0% 
make-4.3             | 507 KB    | ########## | 100% 
make-4.3             | 507 KB    | ########## | 100% 
#7 323.1 
r-data.table-1.14.2  | 2.0 MB    |            |   0% 
r-data.table-1.14.2  | 2.0 MB    | ########## | 100% 
r-data.table-1.14.2  | 2.0 MB    | ########## | 100% 
#7 323.4 
libxcb-1.13          | 391 KB    |            |   0% 
libxcb-1.13          | 391 KB    | ########## | 100% 
libxcb-1.13          | 391 KB    | ########## | 100% 
#7 323.5 
cairo-1.16.0         | 1.5 MB    |            |   0% 
cairo-1.16.0         | 1.5 MB    | ########## | 100% 
cairo-1.16.0         | 1.5 MB    | ########## | 100% 
#7 323.8 
gcc_linux-64-10.4.0  | 29 KB     |            |   0% 
gcc_linux-64-10.4.0  | 29 KB     | ########## | 100% 
#7 323.9 
gfortran_impl_linux- | 14.8 MB   |            |   0% 
gfortran_impl_linux- | 14.8 MB   | #####8     |  58% 
gfortran_impl_linux- | 14.8 MB   | ########## | 100% 
#7 326.2 
libgomp-13.1.0       | 409 KB    |            |   0% 
libgomp-13.1.0       | 409 KB    | ########## | 100% 
#7 326.3 
libiconv-1.17        | 1.4 MB    |            |   0% 
libiconv-1.17        | 1.4 MB    | ########## | 100% 
libiconv-1.17        | 1.4 MB    | ########## | 100% 
#7 326.4 
xorg-renderproto-0.1 | 9 KB      |            |   0% 
xorg-renderproto-0.1 | 9 KB      | ########## | 100% 
#7 326.5 
pycosat-0.6.4        | 108 KB    |            |   0% 
pycosat-0.6.4        | 108 KB    | ########## | 100% 
#7 326.5 
r-stringi-1.7.12     | 882 KB    |            |   0% 
r-stringi-1.7.12     | 882 KB    | ########## | 100% 
#7 326.6 
libgcc-devel_linux-6 | 3.3 MB    |            |   0% 
libgcc-devel_linux-6 | 3.3 MB    | ########## | 100% 
libgcc-devel_linux-6 | 3.3 MB    | ########## | 100% 
#7 327.0 
r-cli-3.6.1          | 1.2 MB    |            |   0% 
r-cli-3.6.1          | 1.2 MB    | ########## | 100% 
#7 327.1 
font-ttf-source-code | 684 KB    |            |   0% 
font-ttf-source-code | 684 KB    | ########## | 100% 
font-ttf-source-code | 684 KB    | ########## | 100% 
#7 327.2 
r-dbi-1.1.3          | 761 KB    |            |   0% 
r-dbi-1.1.3          | 761 KB    | ########## | 100% 
r-dbi-1.1.3          | 761 KB    | ########## | 100% 
#7 327.4 
bioconductor-rhdf5-2 | 2.8 MB    |            |   0% 
bioconductor-rhdf5-2 | 2.8 MB    | ########## | 100% 
bioconductor-rhdf5-2 | 2.8 MB    | ########## | 100% 
#7 327.8 
xorg-libx11-1.8.4    | 810 KB    |            |   0% 
xorg-libx11-1.8.4    | 810 KB    | ########## | 100% 
#7 327.9 
krb5-1.19.3          | 1.4 MB    |            |   0% 
krb5-1.19.3          | 1.4 MB    | ########## | 100% 
krb5-1.19.3          | 1.4 MB    | ########## | 100% 
#7 328.1 
bioconductor-bsgenom | 7.2 MB    |            |   0% 
bioconductor-bsgenom | 7.2 MB    | ########## | 100% 
bioconductor-bsgenom | 7.2 MB    | ########## | 100% 
#7 329.0 
graphite2-1.3.13     | 102 KB    |            |   0% 
graphite2-1.3.13     | 102 KB    | ########## | 100% 
#7 329.0 
idna-2.10            | 52 KB     |            |   0% 
idna-2.10            | 52 KB     | ########## | 100% 
#7 329.1 
lerc-4.0.0           | 275 KB    |            |   0% 
lerc-4.0.0           | 275 KB    | ########## | 100% 
#7 329.1 
pixman-0.40.0        | 627 KB    |            |   0% 
pixman-0.40.0        | 627 KB    | ########## | 100% 
pixman-0.40.0        | 627 KB    | ########## | 100% 
#7 329.3 
bioconductor-dnacopy | 436 KB    |            |   0% 
bioconductor-dnacopy | 436 KB    | ########## | 100% 
#7 329.3 
bioconductor-biocpar | 1.4 MB    |            |   0% 
bioconductor-biocpar | 1.4 MB    | ########## | 100% 
bioconductor-biocpar | 1.4 MB    | ########## | 100% 
#7 329.6 
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#7 344.9 
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#7 347.7 Preparing transaction: ...working... done
#7 350.4 Verifying transaction: ...working... done
#7 354.4 Executing transaction: ...working... done
#7 501.6 ERROR conda.core.link:_execute(699): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.7-r41hdfd78af_2'.
#7 501.6 Rolling back transaction: ...working... done
#7 507.1 class: LinkError
#7 507.1 message:
#7 507.1 post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.7-r41hdfd78af_2
#7 507.1 location of failed script: /opt/conda/bin/.bioconductor-genomeinfodbdata-post-link.sh
#7 507.1 ==> script messages <==
#7 507.1 <None>
#7 507.1 ==> script output <==
#7 507.1 stdout: /opt/conda/share/bioconductor-genomeinfodbdata-1.2.7-2/GenomeInfoDbData_1.2.7.tar.gz: FAILED
#7 507.1 /opt/conda/share/bioconductor-genomeinfodbdata-1.2.7-2/GenomeInfoDbData_1.2.7.tar.gz: FAILED
#7 507.1 Traceback (most recent call last):
#7 507.1   File "/opt/conda/bin/conda-env", line 7, in <module>
#7 507.1     sys.exit(main())
#7 507.1   File "/opt/conda/lib/python3.9/site-packages/conda_env/cli/main.py", line 91, in main
#7 507.1     return conda_exception_handler(do_call, args, parser)
#7 507.1   File "/opt/conda/lib/python3.9/site-packages/conda/exceptions.py", line 1371, in conda_exception_handler
#7 507.1     return_value = exception_handler(func, *args, **kwargs)
#7 507.1   File "/opt/conda/lib/python3.9/site-packages/conda/exceptions.py", line 1082, in __call__
#7 507.1     return self.handle_exception(exc_val, exc_tb)
#7 507.1   File "/opt/conda/lib/python3.9/site-packages/conda/exceptions.py", line 1113, in handle_exception
#7 507.1     return self.handle_application_exception(exc_val, exc_tb)
#7 507.1   File "/opt/conda/lib/python3.9/site-packages/conda/exceptions.py", line 1129, in handle_application_exception
#7 507.1     self._print_conda_exception(exc_val, exc_tb)
#7 507.1   File "/opt/conda/lib/python3.9/site-packages/conda/exceptions.py", line 1133, in _print_conda_exception
#7 507.1     print_conda_exception(exc_val, exc_tb)
#7 507.1   File "/opt/conda/lib/python3.9/site-packages/conda/exceptions.py", line 1056, in print_conda_exception
#7 507.1     stderrlog.error("\n%r\n", exc_val)
#7 507.1   File "/opt/conda/lib/python3.9/logging/__init__.py", line 1475, in error
#7 507.1     self._log(ERROR, msg, args, **kwargs)
#7 507.1   File "/opt/conda/lib/python3.9/logging/__init__.py", line 1589, in _log
#7 507.1     self.handle(record)
#7 507.1   File "/opt/conda/lib/python3.9/logging/__init__.py", line 1598, in handle
#7 507.1     if (not self.disabled) and self.filter(record):
#7 507.1   File "/opt/conda/lib/python3.9/logging/__init__.py", line 806, in filter
#7 507.1     result = f.filter(record)
#7 507.1   File "/opt/conda/lib/python3.9/site-packages/conda/gateways/logging.py", line 60, in filter
#7 507.1     record.msg = record.msg % new_args
#7 507.1   File "/opt/conda/lib/python3.9/site-packages/conda/__init__.py", line [126](https://github.com/Clinical-Genomics/BALSAMIC/actions/runs/5855846314/job/15874424925?pr=1222#step:5:130), in __repr__
#7 [507](https://github.com/Clinical-Genomics/BALSAMIC/actions/runs/5855846314/job/15874424925?pr=1222#step:5:511).1     errs.append(e.__repr__())
#7 507.1   File "/opt/conda/lib/python3.9/site-packages/conda/__init__.py", line 65, in __repr__
#7 507.1     return '%s: %s' % (self.__class__.__name__, text_type(self))
#7 507.1   File "/opt/conda/lib/python3.9/site-packages/conda/__init__.py", line 84, in __str__
#7 507.1     return text_type(self.message % self._kwargs)
#7 507.1 ValueError: unsupported format character 'T' (0x54) at index [847](https://github.com/Clinical-Genomics/BALSAMIC/actions/runs/5855846314/job/15874424925?pr=1222#step:5:851)
#7 ERROR: process "/bin/ash -eo pipefail -c cd /${WORK_DIR}/BALSAMIC/containers/${CONTAINER_NAME}/ && /bin/sh ${CONTAINER_NAME}.sh ${CONTAINER_NAME}" did not complete successfully: exit code: 1
------
 > [4/5] RUN cd /project/BALSAMIC/containers/varcall_cnvkit/ && /bin/sh varcall_cnvkit.sh varcall_cnvkit:
507.1     result = f.filter(record)
507.1   File "/opt/conda/lib/python3.9/site-packages/conda/gateways/logging.py", line 60, in filter
507.1     record.msg = record.msg % new_args
507.1   File "/opt/conda/lib/python3.9/site-packages/conda/__init__.py", line 126, in __repr__
507.1     errs.append(e.__repr__())
507.1   File "/opt/conda/lib/python3.9/site-packages/conda/__init__.py", line 65, in __repr__
507.1     return '%s: %s' % (self.__class__.__name__, text_type(self))
507.1   File "/opt/conda/lib/python3.9/site-packages/conda/__init__.py", line 84, in __str__
507.1     return text_type(self.message % self._kwargs)
507.1 ValueError: unsupported format character 'T' (0x54) at index 847
------
BALSAMIC/containers/varcall_cnvkit/Dockerfile:20
--------------------
  18 |     COPY . /${WORK_DIR}
  19 |     
  20 | >>> RUN cd /${WORK_DIR}/BALSAMIC/containers/${CONTAINER_NAME}/ && /bin/sh ${CONTAINER_NAME}.sh ${CONTAINER_NAME}
  21 |     
  22 |     # Clean work environment
--------------------
ERROR: failed to solve: process "/bin/ash -eo pipefail -c cd /${WORK_DIR}/BALSAMIC/containers/${CONTAINER_NAME}/ && /bin/sh ${CONTAINER_NAME}.sh ${CONTAINER_NAME}" did not complete successfully: exit code: 1
Error: buildx failed with: ERROR: failed to solve: process "/bin/ash -eo pipefail -c cd /${WORK_DIR}/BALSAMIC/containers/${CONTAINER_NAME}/ && /bin/sh ${CONTAINER_NAME}.sh ${CONTAINER_NAME}" did not complete successfully: exit code: 1

@khurrammaqbool khurrammaqbool changed the title fix: cnvkit container feat: add cnvkit Aug 16, 2023
@khurrammaqbool khurrammaqbool marked this pull request as draft August 16, 2023 08:04
@khurrammaqbool
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The container is building now.

@sonarqubecloud
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Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
No Duplication information No Duplication information

@khurrammaqbool khurrammaqbool deleted the fix/cnvkit_container branch August 16, 2023 11:36
@ivadym ivadym restored the fix/cnvkit_container branch August 16, 2023 11:46
@ivadym ivadym deleted the fix/cnvkit_container branch August 16, 2023 15:11
@ivadym ivadym mentioned this pull request Aug 16, 2023
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