I can't reproduce either of these and when I check the resources on the
builders they load successfully so doesn't appear to be a caching issue. I
would expect them to clear up on the next run of the builders. Let's see what
happens on the next run and if they continue to error I can look further into
it.
Lori Shepherd - Kern
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
________________________________
From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Morgan,
Michael via Bioc-devel <bioc-devel@r-project.org>
Sent: Wednesday, June 12, 2024 4:02 AM
To: Dolors Pelegrí <dolors.pele...@isglobal.org>; bioc-devel@r-project.org
<bioc-devel@r-project.org>
Subject: Re: [Bioc-devel] Error in methylclockData package
Dear BioC Team,
I am receiving a similar error from the MouseThymusAgeing package:
> smart.data <- MouseSMARTseqData(samples = "day1")
see ?MouseThymusAgeing and browseVignettes('MouseThymusAgeing') for
documentation
loading from cache
field not found in version - adding
see ?MouseThymusAgeing and browseVignettes('MouseThymusAgeing') for
documentation
loading from cache
Error: failed to load resource
name: EH4592
title: SMARTseq processed counts (day 1)
reason: unknown input format
Execution halted
Which is subsequently propagating through to errors in miloR on nebbiolo1 only
(Windows and Mac build servers are unaffected).
Quitting from lines 47-50 [unnamed-chunk-2] (milo_contrasts.Rmd)
Error: processing vignette 'milo_contrasts.Rmd' failed with diagnostics:
failed to load resource
name: EH4592
title: SMARTseq processed counts (day 1)
reason: unknown input format
Is this an issue with caching files?
Regards
Mike Morgan
Pronouns: He/Him
Lecturer
6.17, Institute of Medical Sciences
School of Medicine, Medical Sciences & Nutrition
University of Aberdeen
Foresterhill
Aberdeen
AB25 2ZD
Tel: 01224 437397
Web:
https://secure-web.cisco.com/1hyURm21NrL7byNpOrxiBZ9a9xz4cDF-n4OMT-AQOSyvTN6cZdOnzmiFftAyFY5_TAfAkcznKKXRhwg85OL8y5rTVUKTkZSnDz8K1qM5AhGqj9NmlSQSagK-Xvbs3-g07pGXOD2gEPTnCTeTPc53ZksF4dO9MmSdZjlGCu2TMh37if3Jzrbadn797r2zkwFjHAb1XIV-kRHSlk_d5FL_yBIo6k0WSmFlmQezPZgEfBkiImWwjod9aUmYieRzOyscrGS3B8YfOlgfumnOan_MpOvkru2IDDo_v1ROoiPGv1j9XNfHnAtahG2q5OgwELJbw/https%3A%2F%2Fwww.abdn.ac.uk%2Fims%2Fresearch%2Fprofiles%2Fmichael.morgan%23research
From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Dolors
Pelegr�dolors.pele...@isglobal.org>
Date: Wednesday, 12 June 2024 at 08:38
To: bioc-devel@r-project.org <bioc-devel@r-project.org>
Subject: [Bioc-devel] Error in methylclockData package
[You don't often get email from dolors.pele...@isglobal.org. Learn why this is
important at
https://secure-web.cisco.com/1TgmSfJggrhMobe5FUzZsmSUYaJwE3XR4wpoxocRyvRv9iSwGznpAO2JlpOVwwf0qZSHrid169q_tCBy4Xo4pjJE9HMepdEfYOjkMuy9AO3OENDtx0qAfIWW-iYiwa_1rPxf04aIgt0oU0fe53WI_UftEAO09PpN9gh2OMEkqFBCPbKQw4lsHnVQY8TdRsFfFiP9HxucmLwi5ByEjFDz0O5QsHyVKv_pOySsgo5d-h1ldjJKfCsT3gEhawjzyd1f_iooruyJfJ2dNErWDGqSPXQSGm-N6oJ_7vEUWcITHQgC3FBM-gSGBFNunEVg-sPkl/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification
]
CAUTION: External email. Ensure this message is from a trusted source and
exercise caution before clicking links/opening attachments.
Dear Bioconductor team,
I have seen that the methylclockData package gives an error when loading
the EH6082 resource, the error is:
get_TestDataset()
see ?methylclockData and browseVignettes('methylclockData') for
documentation
loading from cache
Warning in grepl("RD[ABX][2-9]\n", magic) :
unable to translate '<89>HDF
' to a wide string
Warning in grepl("RD[ABX][2-9]\n", magic) : input string 1 is invalid
Warning in grepl("RD[ABX][2-9]\r", magic) :
unable to translate '<89>HDF
' to a wide string
Warning in grepl("RD[ABX][2-9]\r", magic) : input string 1 is invalid
Warning in gsub("[\n\r]*", "", magic) :
unable to translate '<89>HDF
' to a wide string
Error: failed to load resource
name: EH6082
title: Test Dataset
reason: error in evaluating the argument 'x' in selecting a method for
function 'get': input string 1 is invalid
Execution halted
Full Bioconductor Checks:
https://bioconductor.org/checkResults/3.19/data-experiment-LATEST/methylclockData/nebbiolo1-checksrc.html<https://secure-web.cisco.com/1jf9ytfpmFmocyAfOpBw_grzcU1oGr3iMOG6l_DdAq3dFaXdA3mxJtS3itQFxhW5HqVb5DBmknP6RrWxXs_am2zYwBdHCwVEP5RiqO03tGY2lfgcpsZqPcpHwyzetaTDW5KHZMdggG9y2Fwdz4j1nZfPKukOL-oZDF0Ies6Zv2wlXf3mZZd7gZet2L6OujW_bIzdrxd4Kn1OVdLk8eFpIbs8RWjuOxENmQYJ6jt9sNlLVw2Q01eY8Z0vXXEyRZqr5vfCtbhoKVhtwm6J-1iwDzTLUypFqzRm-Cy8_YiNehVHdyw6rhkcK3Tmd_R4QQf3b/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.19%2Fdata-experiment-LATEST%2FmethylclockData%2Fnebbiolo1-checksrc.html>
I don't know the reason or how I could solve it, I've searched the
distribution list and I haven't found any similar error. Could you please
give me some guidance to solve the error?
Best,
--
Dolors Pelegr�is�ioinformatics
*IS**Global*
Barcelona Institute for Global Health
Barcelona Biomedical Research Park (PRBB)
Doctor Aiguader 88
E-08003 Barcelona, Spain
Tel. +34 93 2147351
dolors.pele...@isglobal.org <samuel.espi...@isglobal.org>
http://www.isglobal.org/<http://secure-web.cisco.com/1MjTzDBJOl_XjIdIYw9hkFhyW5dqUpDvLGnL2dOGCfvlyvBXLDPcp6fPPcvbZdL-fdoiyRVaQdEzmnaKPPYxGDEuHWtQyOJ7AHANyti1St-L7WV6drXL-ujNVM2UaFfo5CfB7B2Qn-VWiNlcZuMmFx71Q4VYKzznUI6Tzuhy8AEuhe0pY97OAqs9mF6FxPx4GZHNjSgHcvtTu3g_3xeFTlNoC0mNRE84t3i30nnqPNEkuSMZhpSdvwEX0xcHQifeBIEF82b0eHfkQqQyWJ825u3oV3K10pEOKRKGk5HU1wPWYRX1rhUDRiTZ3ySU6fzFR/http%3A%2F%2Fwww.isglobal.org%2F>
--
This message is intended exclusively for its addressee and may contain
information that is CONFIDENTIAL and protected by professional privilege.
If
you are not the intended recipient you are hereby notified that any
dissemination, copy or disclosure of this communication is strictly
prohibited
by law. If this message has been received in error, please
immediately notify
us via e-mail and delete it.
DATA PROTECTION. We
inform you that your personal data, including your
e-mail address and data
included in your email correspondence, are included in
the ISGlobal
Foundation files. Your personal data will be used for the purpose
of
contacting you and sending information on the activities of the above
foundations. You can exercise your rights of access, rectification,
cancellation and opposition by contacting the following address:
l...@isglobal.org <mailto:l...@isglobal.org>. ISGlobal
Privacy Policy at
http://www.isglobal.org/<http://secure-web.cisco.com/1MjTzDBJOl_XjIdIYw9hkFhyW5dqUpDvLGnL2dOGCfvlyvBXLDPcp6fPPcvbZdL-fdoiyRVaQdEzmnaKPPYxGDEuHWtQyOJ7AHANyti1St-L7WV6drXL-ujNVM2UaFfo5CfB7B2Qn-VWiNlcZuMmFx71Q4VYKzznUI6Tzuhy8AEuhe0pY97OAqs9mF6FxPx4GZHNjSgHcvtTu3g_3xeFTlNoC0mNRE84t3i30nnqPNEkuSMZhpSdvwEX0xcHQifeBIEF82b0eHfkQqQyWJ825u3oV3K10pEOKRKGk5HU1wPWYRX1rhUDRiTZ3ySU6fzFR/http%3A%2F%2Fwww.isglobal.org%2F>
<http://www.isglobal.org/<http://secure-web.cisco.com/1MjTzDBJOl_XjIdIYw9hkFhyW5dqUpDvLGnL2dOGCfvlyvBXLDPcp6fPPcvbZdL-fdoiyRVaQdEzmnaKPPYxGDEuHWtQyOJ7AHANyti1St-L7WV6drXL-ujNVM2UaFfo5CfB7B2Qn-VWiNlcZuMmFx71Q4VYKzznUI6Tzuhy8AEuhe0pY97OAqs9mF6FxPx4GZHNjSgHcvtTu3g_3xeFTlNoC0mNRE84t3i30nnqPNEkuSMZhpSdvwEX0xcHQifeBIEF82b0eHfkQqQyWJ825u3oV3K10pEOKRKGk5HU1wPWYRX1rhUDRiTZ3ySU6fzFR/http%3A%2F%2Fwww.isglobal.org%2F>>.
-----------------------------------------------------------------------------------------------------------------------------
CONFIDENCIALIDAD. Este mensaje y sus anexos se dirigen exclusivamente a
su
destinatario y puede contener informaci�onfidencial, por lo que la
utilizaci�divulgaci�/o copia sin autorizaci�st�rohibida por la
legislaci�igente. Si ha recibido este mensaje por error, le rogamos lo
comunique
inmediatamente por esta misma v�y proceda a su destrucci�
PROTECCI� DE DATOS. Sus datos de car�er personal utilizados en este
env� incluida su direcci�e e-mail, forman parte de ficheros de
titularidad
de la Fundaci�SGlobal para cualquier
finalidades de
contacto, relaci�nstitucional y/o env�de informaci�obre
sus
actividades. Los datos que usted nos pueda facilitar contestando este
correo quedar�incorporados en los correspondientes ficheros, autorizando
el
uso de su direcci�e e-mail para las finalidades citadas. Puede
ejercer los
derechos de acceso, rectificaci�cancelaci� oposici�irigi�ose a
l...@isglobal.org <mailto:l...@isglobal.org>* *. Pol�ca de
privacidad
en
http://www.isglobal.org/<http://secure-web.cisco.com/1MjTzDBJOl_XjIdIYw9hkFhyW5dqUpDvLGnL2dOGCfvlyvBXLDPcp6fPPcvbZdL-fdoiyRVaQdEzmnaKPPYxGDEuHWtQyOJ7AHANyti1St-L7WV6drXL-ujNVM2UaFfo5CfB7B2Qn-VWiNlcZuMmFx71Q4VYKzznUI6Tzuhy8AEuhe0pY97OAqs9mF6FxPx4GZHNjSgHcvtTu3g_3xeFTlNoC0mNRE84t3i30nnqPNEkuSMZhpSdvwEX0xcHQifeBIEF82b0eHfkQqQyWJ825u3oV3K10pEOKRKGk5HU1wPWYRX1rhUDRiTZ3ySU6fzFR/http%3A%2F%2Fwww.isglobal.org%2F>
<http://www.isglobal.org/<http://secure-web.cisco.com/1MjTzDBJOl_XjIdIYw9hkFhyW5dqUpDvLGnL2dOGCfvlyvBXLDPcp6fPPcvbZdL-fdoiyRVaQdEzmnaKPPYxGDEuHWtQyOJ7AHANyti1St-L7WV6drXL-ujNVM2UaFfo5CfB7B2Qn-VWiNlcZuMmFx71Q4VYKzznUI6Tzuhy8AEuhe0pY97OAqs9mF6FxPx4GZHNjSgHcvtTu3g_3xeFTlNoC0mNRE84t3i30nnqPNEkuSMZhpSdvwEX0xcHQifeBIEF82b0eHfkQqQyWJ825u3oV3K10pEOKRKGk5HU1wPWYRX1rhUDRiTZ3ySU6fzFR/http%3A%2F%2Fwww.isglobal.org%2F>>.
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel<https://secure-web.cisco.com/1DimnD3Q0u8zBHoEG4I-xyOfhzntWs4NNvy-xVjMfT_fPWgSQLdhZLKwmxQ9lXXJdVUvt0FGx-L_0pRDBWc48V4Nyd-J1cHHdoGBaw-QJR0xjHgBTJIobGa7SWlmokTXcO3hSD4Ei7hvj1SsPAGffNy_EazjUlTVjYnde8W-gmc-JgxkVHgG2-oPdZqA3_dKi-jy_C4s_PTGfBYIQAPXpU1JgLb4olat0xzsRPAHzJ25WYN6VSLOliebh0-avZeUM-POmPnGIz8-OGu5bmeeCI_fIV5_Y4lHhqMqo3OihmGg7xmx7tn50JZM4jKXulP_w/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel>
The University of Aberdeen is a charity registered in Scotland, No SC013683.
Tha Oilthigh Obar Dheathain na charthannas cl�ichte ann an Alba, �r. SC013683.
[[alternative HTML version deleted]]
This email message may contain legally privileged and/or confidential
information. If you are not the intended recipient(s), or the employee or
agent responsible for the delivery of this message to the intended
recipient(s), you are hereby notified that any disclosure, copying,
distribution, or use of this email message is prohibited. If you have received
this message in error, please notify the sender immediately by e-mail and
delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
