[Bioc-devel] index of Bioc repository unavailable - Bioc-devel

Tue, May 28, 2019 1:04 PM #

Travis recently started to fail for Bioc devel (see [0] and [1] for another possibly related report), which seems to related to a warning in BiocManager::available():

[1] ?3.10?

Warning: unable to access index for repository https://bioconductor.org/packages/3.10/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.10/data/annotation/src/contrib/PACKAGES'
 chr [1:16400] "a4" "a4Base" "a4Classif" "a4Core" "a4Preproc" "a4Reporting" ...

Is this a temporary or known issue?

Thanks in advance.

Laurent

[0] https://travis-ci.org/lgatto/Features/jobs/538412208
[1] https://travis-ci.community/t/error-bioconductor-version-not-changed/3491

Hervé Pagès

Tue, May 28, 2019 1:24 PM #

Hi Laurent,

This is temporary. We're in the process of creating the 3.10 annotation 
repo by "forking" the 3.9 annotation repo. As part of this process, we 
run a script that generates the PACKAGES index for the new 3.10
annotation repo. The process will take a few more hours before it
completes. Then this warning should go away.

Sorry for the inconvenience.

Cheers,
H.

On 5/28/19 13:04, Laurent Gatto wrote:

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https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIF-g&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=UAmM0hNRENFU1Y4T29z5hJJHFLKXbyWj2W8KtGaqZEE&s=nYwhpdHm_ENLuhTqIli7MtPUPdf8EKlcLuXvxqiI_sE&e=

Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

Laurent Gatto

Tue, May 28, 2019 1:28 PM #

No worries at all. Thank you for letting me know.

Laurent

From: Pages, Herve <hpages at fredhutch.org>
Sent: 28 May 2019 22:24
To: Laurent Gatto; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] index of Bioc repository unavailable

Hi Laurent,

This is temporary. We're in the process of creating the 3.10 annotation
repo by "forking" the 3.9 annotation repo. As part of this process, we
run a script that generates the PACKAGES index for the new 3.10
annotation repo. The process will take a few more hours before it
completes. Then this warning should go away.

Sorry for the inconvenience.

Cheers,
H.

On 5/28/19 13:04, Laurent Gatto wrote:
> Travis recently started to fail for Bioc devel (see [0] and [1] for another possibly related report), which seems to related to a warning in BiocManager::available():
>
>> BiocManager::version()
> [1] ?3.10?
>> str(BiocManager::available())
> Warning: unable to access index for repository https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_3.10_data_annotation_src_contrib&d=DwIF-g&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=UAmM0hNRENFU1Y4T29z5hJJHFLKXbyWj2W8KtGaqZEE&s=I-j2hOB7kAvw9DSOUy8nHyxKb5KH19tqAAxuwZ5E8HY&e= :
>    cannot open URL 'https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_3.10_data_annotation_src_contrib_PACKAGES&d=DwIF-g&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=UAmM0hNRENFU1Y4T29z5hJJHFLKXbyWj2W8KtGaqZEE&s=E4iryKtRU-QLj7b-IdceimIOQCK_Ch9bdKzN-YgZMwE&e= '
>   chr [1:16400] "a4" "a4Base" "a4Classif" "a4Core" "a4Preproc" "a4Reporting" ...
>
> Is this a temporary or known issue?
>
> Thanks in advance.
>
> Laurent
>
> [0] https://urldefense.proofpoint.com/v2/url?u=https-3A__travis-2Dci.org_lgatto_Features_jobs_538412208&d=DwIF-g&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=UAmM0hNRENFU1Y4T29z5hJJHFLKXbyWj2W8KtGaqZEE&s=GPakdUkHa8x0dEHAyNi_W5Qup4XJjADUPM2Dk_bdmN4&e=
> [1] https://urldefense.proofpoint.com/v2/url?u=https-3A__travis-2Dci.community_t_error-2Dbioconductor-2Dversion-2Dnot-2Dchanged_3491&d=DwIF-g&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=UAmM0hNRENFU1Y4T29z5hJJHFLKXbyWj2W8KtGaqZEE&s=MN6IdiDrYMIta6JGJlEJ19qaks1n9GKa4h6zMsFtwhQ&e=
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIF-g&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=UAmM0hNRENFU1Y4T29z5hJJHFLKXbyWj2W8KtGaqZEE&s=nYwhpdHm_ENLuhTqIli7MtPUPdf8EKlcLuXvxqiI_sE&e=
>

--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319