cp: cannot open `/tmp/_circleci_local_build_repo/./nohup.out' for reading: Permission denied

Build Environment
1 
$ circleci build

====>> Spin up Environment
Build-agent version 0.0.5895-01cdb92 (2018-05-29T20:07:10+0000)
Starting container bioconda/bioconda-utils-build-env
  using image bioconda/bioconda-utils-build-env@sha256:15ee49e7dea59105b90a89660b385b0367eca5a533a2816ab9984d545d6c45dd

Using build environment variables:
  BASH_ENV=/tmp/.bash_env-localbuild-1533496688
  CI=true
  CIRCLECI=true
  CIRCLE_BRANCH=master
  CIRCLE_BUILD_NUM=
  CIRCLE_JOB=build
  CIRCLE_NODE_INDEX=0
  CIRCLE_NODE_TOTAL=1
  CIRCLE_REPOSITORY_URL=https://github.com/bio-nim/bioconda-recipes
  CIRCLE_SHA1=74b4e4fabb57ac401041fc3b0ee2455ef9560a53
  CIRCLE_SHELL_ENV=/tmp/.bash_env-localbuild-1533496688
  CIRCLE_WORKING_DIRECTORY=~/project

====>> Checkout code
  #!/bin/sh
mkdir -p /root/project && cp -r /tmp/_circleci_local_build_repo/. /root/project
cp: cannot open `/tmp/_circleci_local_build_repo/./nohup.out' for reading: Permission denied
2

Would you edit some introductory text into this question, to come before the links/code? My experience on Stack Overflow is that posting a link without any context/preamble is not always received well. Volunteers will say “there is no question here”.

3

I don’t know how more succinctly to put it. That’s the command I run and the output I see.

I am following this guide:
https://bioconda.github.io/contribute-a-recipe.html#test-locally

It may be more of a bioconda problem or a docker problem, but I can’t tell. I’m hoping someone else has seen this and knows my mistake.

4

Much better, thanks. My other ethic when reading/helping with questions is “I’ll expend upon this question the effort that was expended to post it”, and thus if a question is merely a go-fetch from somewhere else, I tend to skip. On the web there’s more questions than willing helpers, so that may be worth bearing in mind :slightly_smiling_face:.

5

Oh, I’ve made some progress! I had an unreadable file nohup.out in my working directory because of earlier attempts to get Docker running on OSX. That was the main problem.

I still have a circleci-specific problem, I think:

$ time circleci build

====>> Spin up Environment
Build-agent version 0.0.5895-01cdb92 (2018-05-29T20:07:10+0000)
Starting container bioconda/bioconda-utils-build-env
  using image bioconda/bioconda-utils-build-env@sha256:15ee49e7dea59105b90a89660b385b0367eca5a533a2816ab9984d545d6c45dd

Using build environment variables:
  BASH_ENV=/tmp/.bash_env-localbuild-1533576931
  CI=true
  CIRCLECI=true
  CIRCLE_BRANCH=master
  CIRCLE_BUILD_NUM=
  CIRCLE_JOB=build
  CIRCLE_NODE_INDEX=0
  CIRCLE_NODE_TOTAL=1
  CIRCLE_REPOSITORY_URL=https://github.com/bio-nim/bioconda-recipes
  CIRCLE_SHA1=74b4e4fabb57ac401041fc3b0ee2455ef9560a53
  CIRCLE_SHELL_ENV=/tmp/.bash_env-localbuild-1533576931
  CIRCLE_WORKING_DIRECTORY=~/project

====>> Checkout code
  #!/bin/sh
mkdir -p /root/project && cp -r /tmp/_circleci_local_build_repo/. /root/project
====>> Setup ssh
  #!/bin/bash -eo pipefail
mkdir -p ~/.ssh
ssh-keyscan -H github.com >> ~/.ssh/known_hosts

# github.com SSH-2.0-libssh_0.7.0
====>> Setup base system
  #!/bin/bash -eo pipefail
cat >> $BASH_ENV <<EOF
if [[ \$- == *u* ]] ; then
    set +u ; . /tmp/repo/docker-entrypoint-source ; set -u
else
    . /tmp/repo/docker-entrypoint-source
fi
EOF

====>> Download common definitions
  #!/bin/bash -eo pipefail
curl -s https://raw.githubusercontent.com/bioconda/bioconda-common/master/common.sh > .circleci/common.sh

====>> Setup bioconda-utils
  #!/bin/bash -eo pipefail
.circleci/setup.sh
remote: Counting objects: 120, done.
remote: Total 120 (delta 58), reused 58 (delta 58), pack-reused 62
Receiving objects: 100% (120/120), 157.24 KiB | 2.76 MiB/s, done.
Resolving deltas: 100% (59/59), completed with 24 local objects.
From https://github.com/bioconda/bioconda-recipes
 * [new branch]          master     -> __upstream__rsFJF6ejQe/master
fatal: Refusing to fetch into current branch refs/heads/master of non-bare repository
====>> Linting
  #!/bin/bash -eo pipefail
bioconda-utils lint recipes config.yml \
--loglevel debug --full-report \
--git-range master HEAD

17:37:25 BIOCONDA INFO Recipes newly unblacklisted:

17:37:25 BIOCONDA INFO No recipe modified according to git, exiting.
====>> Testing
  #!/bin/bash -eo pipefail
bioconda-utils build recipes config.yml \
--git-range master HEAD \
--prelint

17:37:27 BIOCONDA INFO Recipes newly unblacklisted:

17:37:27 BIOCONDA INFO No recipe modified according to git, exiting.
Success!

Why does it not see my local changes? The following does see my changes:

bioconda-utils build recipes config.yml --mulled-test --docker --git-range master
6

Great update! I’m not familiar with Bioconda or what it does, but I wonder if there is an issue to do with folder confusion. I am wondering if everything is run in a cwd of /root but you’ve checked out to /root/project? I would suggest doing a (temporary) run step of pwd; ls -l prior to your failing command, just to check this.

Also, this looks like it needs attention:

fatal: Refusing to fetch into current branch refs/heads/master of non-bare repository

7

So those are all bioconda-utils problems? But I am able to run bioconda-utls directly in my local shell. Hmmm… Well, thanks for your suggestions.

8

I don’t understand your question - my suggestions above could be described either as Linux or Git or CircleCI problems. I am not sure it matters too much though; give them both a try, and let me know how you get on :smiley_cat: .

9

Ok. I changed one of the run steps to “pwd; ls -larth”:

====>> Setup bioconda-utils
  #!/bin/bash -eo pipefail
pwd; ls -larth
/root/project
total 384K
-rwxr-xr-x    1 root root 4.2K Aug  6 19:35 bootstrap.py
drwxr-xr-x    9 root root 4.0K Aug  6 19:37 .git
drwxr-xr-x    2 root root 4.0K Aug  6 19:37 .circleci
-rw-r--r--    1 root root 7.1K Aug  6 19:37 oc3
...

It’s clearly a copy of my own working directory, which is a git-clone. So I’ve added set -vx to .circleci/setup.sh… I guess the problem is that Bioconda folks expect this to be run a different way. Not exactly a bug.

1 Like
10

chmod -R 777 ./workingDirectory works for me

11

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