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Ryan C. Thompson DarwinAwardWinner Icahn School of Medicine at Mount Sinai NYC area Bioinformatics analyst

DarwinAwardWinner/amx 123

An alternative M-x interface for Emacs.

c9s/App-gh 53

GitHub Command-line Utility.

DarwinAwardWinner/CD4-csaw 16

Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set

DarwinAwardWinner/crm-custom 8

Alternate completing-read-multiple that uses completing-read

DarwinAwardWinner/Dist-Zilla-Plugin-CopyFilesFromBuild 5

Copy specific files after building (for SCM inclusion, etc.)

DarwinAwardWinner/adjust-parens 4

Indent and dedent Lisp code, automatically adjust close parens

DarwinAwardWinner/Dist-Zilla-Plugin-ReadmeAnyFromPod 3

Automatically convert POD to a README for Dist::Zilla

DarwinAwardWinner/App-gh 2

Powerful GitHub Helper Utility in Perl.

DarwinAwardWinner/BiocParallel 2

Bioconductor facilities for parallel evaluation (experimental)

DarwinAwardWinner/cd4-histone-paper-code 2

Public release of most of the data analysis code for Lamere et. al. 2016

issue commentBioconductor/BiocParallel

Error in serialize(data, node$con) : error writing to connection

Please see my previous comment, I cannot be more helpful without a reproducible example.

yuan596

comment created time in 13 hours

issue commentBioconductor/BiocParallel

Error in serialize(data, node$con) : error writing to connection

hi, I want to speed up code execution by using this package.But this error occurs frequently, and it resumes normal operation after a while. I don't know why. thank you~

------------------ 原始邮件 ------------------ 发件人: "Bioconductor/BiocParallel" ***@***.***>; 发送时间: 2021年6月17日(星期四) 晚上10:03 ***@***.***>; ***@***.******@***.***>; 主题: Re: [Bioconductor/BiocParallel] Error in serialize(data, node$con) : error writing to connection (#143)

This could be because the data (input or return) is too large. Pass less data, e.g., a path to a file on your system instead of the contents of the file in memory.

It could also be that an error occurs in your code. Try running with register(SerialParam()) instead of in parallel.

Please report back here if this helps.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

yuan596

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issue commentBioconductor/BiocParallel

Error in serialize(data, node$con) : error writing to connection

This could be because the data (input or return) is too large. Pass less data, e.g., a path to a file on your system instead of the contents of the file in memory.

It could also be that an error occurs in your code. Try running with register(SerialParam()) instead of in parallel.

Please report back here if this helps.

yuan596

comment created time in a day

issue openedBioconductor/BiocParallel

Error in serialize(data, node$con) : error writing to connection

hello,I have a problem when use the BiocParallel package.When I use the bplappy() function,it reports an error and terminates the code operation: Error in serialize(data, node$con) : 链结书写发生了错误 Calls: local ... .send -> <Anonymous> -> sendData.SOCKnode -> serialize how can I solve this problem? Thank you ~

created time in a day

PR opened dimitri/el-get

Fix emms recipe

Without this commit, installation of emms fails with:

make: *** No rule to make target 'autoloads'.  Stop.
+2 -3

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Stephan Creutz

commit sha ccca97f2264b64a0474fcc68378ebeb10b72f1e7

Replace cl by cl-lib Since Emacs 27 the package cl is deprecated, the replacement is cl-lib, which is available since Emacs 24.3. This patch replaces cl by cl-lib and drops support for Emacs versions less than 24.3. Dropping older Emacsen is required, because cl-lib is a builtin starting from version 24.3 and doesn't need an extra package from ELPA. Testcases for past issues still contain cl. Most of them seem to be broken and need further investigation. This patch is tested with test/run-ert.sh, which outputs: Ran 10 tests, 10 results as expected, 0 unexpected (2021-01-30 13:24:54+0100, 0.672122 sec) 1 expected failures and manually by daily usage for a month now.

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Stephan Creutz

commit sha 7bc810803de735232e69e8326f17dcbc8eefed76

Use cl-mapcan instead of mapcan The function mapcan exists outside cl since Emacs 26.1.

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Stephan Creutz

commit sha 5a4fa85f40d77a93cbf102639f3a30c77bc0a2f6

Remove Emacs 23.4 from Github Actions test workflow This change is required, because Emacs 23 doesn't natively provide cl-lib.

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Stephan Creutz

commit sha 21a75ba79b4188c32866c4bffe83992722fbaa84

Fix missing requirements

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Stephan Creutz

commit sha ac986792c35638bdcfc8b69ecd5a4132d4a82668

Fix position of define-obsolete-variable-alias

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Stephan Creutz

commit sha 4d6f30d165cabe20f6e980ec5db1f0b049307f05

Fix lambda invocation for Emacs 28

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Stephan Creutz

commit sha ebaa979d2b601a5fefc3a50fc57a662f29784dad

Fix doc string for el-get-verbose Emacs 28 enforces 80 characters per doc string line.

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INA Lintaro

commit sha ec135b5353867ce3564a675e99024944b834395d

Merge pull request #2802 from stephan-cr/replace-cl Replace cl by cl-lib

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PR merged dimitri/el-get

Replace cl by cl-lib

Since Emacs 27 the package cl is deprecated, the replacement is cl-lib, which is available since Emacs 24.3.

This patch replaces cl by cl-lib and drops support for Emacs versions less than 24.3. Dropping older Emacsen is required, because cl-lib is a builtin starting from version 24.3 and doesn't need an extra package from ELPA.

Testcases for past issues (in test/issues) still contain cl. Most of them seem to be broken and need further investigation.

This patch is tested with test/run-ert.sh, which outputs:

Ran 10 tests, 10 results as expected, 0 unexpected (2021-01-30 13:24:54+0100, 0.672122 sec)
1 expected failures

and manually by daily usage for a month now.

This PR addresses issue #2792.

+431 -413

6 comments

28 changed files

stephan-cr

pr closed time in 5 days

PR closed dimitri/el-get

Add Emacs 27.1 to CI

Build el-get for Emacs 27.1 as well.

+1 -0

6 comments

1 changed file

stephan-cr

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pull request commentdimitri/el-get

Add Emacs 27.1 to CI

Closed, because el-get moved to Github Actions.

stephan-cr

comment created time in 5 days

pull request commentdimitri/el-get

Replace cl by cl-lib

@tarao Fixed all compilation errors. The PR doesn't look nice, because it fixes several unrelated errors, due to unreliable CI. I created a follow-up issue to fix the remaining compilation errors.

stephan-cr

comment created time in 5 days

issue openeddimitri/el-get

Byte compilation should be separately done for each file

$ byte-compile -Werror *.el

... nothing.

$ for i in *.el ; do byte-compile -Werror $i ; done

In toplevel form:
el-get-byte-compile.el:64:9:Error: reference to free variable ‘el-get-byte-compile’

In toplevel form:
el-get-core.el:42:9:Error: reference to free variable ‘el-get-verbose’

In toplevel form:
el-get-dependencies.el:186:1:Error: the function ‘el-get-read-package-with-status’ is not known to be defined.

In toplevel form:
el-get.el:199:28:Error: The compiler ignores ‘autoload’ except at top level.  You should
     probably put the autoload of the macro ‘el-get-bundle’ at top-level.

In toplevel form:
el-get-list-packages.el:452:1:Error: the following functions are not known to be defined: el-get-recipe-filename, el-get-package-type, el-get-package-def, el-get-package-method, el-get-version-to-list, el-get-recipe-pprint, el-get-read-all-recipes

In toplevel form:
el-get-methods.el:46:11:Error: reference to free variable ‘el-get-allow-insecure’

In toplevel form:
el-get-recipes.el:331:1:Error: the function ‘el-get-github-parse-user-and-repo’ is not known to be defined.

In toplevel form:
el-get-status.el:81:21:Error: reference to free variable ‘el-get-status-file’

This issue causes spurious CI failures.

created time in 5 days

pull request commentdimitri/el-get

Replace cl by cl-lib

@tarao For some strange reason https://github.com/dimitri/el-get/pull/2838/checks?check_run_id=2813750015 gives:

In toplevel form:
methods/el-get-go.el:42:43:Error: reference to free variable ‘el-get-dir’

I cannot reproduce it locally, but I fix that nevertheless.

stephan-cr

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pull request commentdimitri/el-get

Replace cl by cl-lib

@stephan-cr I think I could fix it now. It seems that byte-compilation tests should run if there is change outside recipe/.

Here are results from a test pull request; I think these are what you have expected: https://github.com/dimitri/el-get/pull/2838/checks?check_run_id=2813750015

stephan-cr

comment created time in 5 days

pull request commentdimitri/el-get

(DO NOT MERGE) Test GitHub Actions

Strangely, running

$ byte-compile -Werror *.el methods/*.el

gives me

Source file ‘/home/stephan/.emacs.d/el-get/el-get/el-get-notify.el’ newer than byte-compiled file; using older file

In toplevel form:
el-get-notify.el:24:1:Error: Alias for ‘el-get-growl-notify-path’ should be declared before its referent

Neither Travis-CI nor GH do fail for this.

tarao

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PR closed dimitri/el-get

(DO NOT MERGE) Test GitHub Actions
+1 -0

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tarao

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pull request commentdimitri/el-get

(DO NOT MERGE) Test GitHub Actions

It looks good now.

tarao

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tarao

commit sha 99c828f01dd9c0195bdd96130085ba37dc35c761

Prefer .pull_request.base.sha than .before in case of force-push.

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tarao

commit sha 792592180304f116e475903b45dcf2d3963d0a26

jq returns null for missing fields.

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PR opened dimitri/el-get

(DO NOT MERGE) Test GitHub Actions
+1 -0

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tarao

commit sha 4165fefe168db6bcc7c94f303ef080567240fb91

Print event.json.

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tarao

commit sha 76340ecd117b34eca2a2c9496c22e2795d3bd595

Reconstruct COMMIT_RANGE from GitHub event JSON.

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INA Lintaro

commit sha e67328edfa10d2b83ae5dd85bd7e7783d07ffff0

Merge pull request #2837 from tarao/fix-github-actions-commit-range Fix GitHub Actions COMMIT_RANGE

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PR opened dimitri/el-get

Fix GitHub Actions COMMIT_RANGE
+16 -2

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pull request commentdimitri/el-get

Replace cl by cl-lib

@tarao It must be something different, the message fatal: origin/master...HEAD: no merge base appears for the successful ones as well.

stephan-cr

comment created time in 6 days

pull request commentdimitri/el-get

Replace cl by cl-lib

Aha, I guess it is about a workaround replacing TRAVIS_COMMIT_RANGE. I will fix it but it may take some time.

stephan-cr

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pull request commentdimitri/el-get

Replace cl by cl-lib

Rebased to current master. Some check for Emacs 24.5 fails with fatal: origin/master...HEAD: no merge base.

stephan-cr

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pull request commentdimitri/el-get

Add Emacs 27.1 to CI

@stephan-cr

I had the same question and looked into the test code. It seems that byte-compilation is skipped for recipe-only changes (non-code changes) except on Emacs 24.5. So, it should do byte-compilation test on your replace-cl branch after rebasing master branch.

stephan-cr

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pull request commentdimitri/el-get

Add Emacs 27.1 to CI

@tarao I saw your changes. Great move! But I wonder why byte-compile -Werror *.el methods/*.el doesn't fail for Emacs 27.2.

stephan-cr

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tarao

commit sha bffcd8e90bc5fbe025486f5e735bd7b57a4740dc

typo

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pull request commentdimitri/el-get

Add Emacs 27.1 to CI

@stephan-cr I've added Emacs 27.2 to CI during switching from Travis CI to GitHub Actions in #2836. Could you continue #2802 with this?

stephan-cr

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PR merged dimitri/el-get

Run tests on GitHub Actions
+63 -31

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tarao

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