[Bioc-devel] methylclock package error in devel branch with Palomino4

Kern, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Tue Sep 13 13:37:14 CEST 2022

I have reset the cache for that data object and appears to load correctly now.
It should be set for tomorrow's build report. Thur at the latest.

Please be advised that there is a  ERROR in the methyclockData package that may or may not also be related.


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-bounces using r-project.org> on behalf of Dolors Pelegr� <dolors.pelegri using isglobal.org>
Sent: Tuesday, September 13, 2022 4:33 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] methylclock package error in devel branch with Palomino4


I have seen that the methylclock package does not build correctly in the
devel repository with the Palomino4 server.
The error it shows is related to resources

snapshotDate(): 2022-08-23
see ?methylclockData and browseVignettes('methylclockData') for documentation
loading from cache
Warning: file '22fc76c563d9_7418' has magic number 'SQLit'
  Use of save versions prior to 2 is deprecated
Quitting from lines 210-214 (methylclock.Rmd)
Error: processing vignette 'methylclock.Rmd' failed with diagnostics:
failed to load resource
  name: EH7368
  title: Coefficients EN clock
  reason: error in evaluating the argument 'x' in selecting a method
for function 'get': bad restore file magic number (file may be
corrupted) -- no data loaded
--- failed re-building 'methylclock.Rmd'

SUMMARY: processing the following file failed:

Error: Vignette re-building failed.
Execution halted

The error only occurs on this server and I don't know if it is due to the
cache or the error may be related to the methylclockData packet

Any help would be greatly appreciated


Dolors Pelegr� Sis�



Barcelona Institute for Global Health

Barcelona Biomedical Research Park (PRBB)

Doctor Aiguader 88

E-08003 Barcelona, Spain

Tel. +34 93 2147351

dolors.pelegri using isglobal.org <samuel.espinal using isglobal.org>



This message is intended exclusively for its addressee and may contain
information that is CONFIDENTIAL and protected by professional privilege.
you are not the intended recipient you are hereby notified that any
dissemination, copy or disclosure of this communication is strictly
by law. If this message has been received in error, please
immediately notify
us via e-mail and delete it.

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
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:
lopd using isglobal.org <mailto:lopd using isglobal.org>. ISGlobal
Privacy Policy at
http://secure-web.cisco.com/1jYETCf8Z31mlXyEguj5N_4uRYqLgUzUHJ8zg3l8Y-HNg-qmPlR42_sLritOL8uyojzNYQSZAAQtaxkCs6Zab0JLnhS4uZ_cyP4punoMuz-iCONz0xcozMsaz0d1XhZammfouvRSiQ9TAU9YwRhn5wlQ2JqDvR5boanPU6LmqISZPQ2kpjK4w5yPnxjishrbMvR0ZZFavIjMOuYj4h9rY9TZy7ECyHkSfhIWv4O3PcPuVYoWnwBFeYxVeA_hTyxHFetioldkLbyONQFpUVpyPgXAHjZlKu0DZ-JQA_S_0vy3h_ge-6kgecwpGdaZgPd51/http%3A%2F%2Fwww.isglobal.org <http://secure-web.cisco.com/1IP90dh07vlVZJb49MNYD5PAAbqci8TPvWXhLl18hjJvjKc-W1tJ30bY5bAKRf0AFzly80g7KL4d-0DdDL6H9DW4uEr2GNgDAk_39Vt-l_nTM0a0bJIepy9MjxBHXbP42_XYLskYkz0jX62et39hHKTSj3jCrOHlcc2wTMyHUYA1C9YL9zgTy4Dv39In8duSS_QxXH2tAHEmjsyIBi9ue1V2Y7b2k8yMHUfRyDqFBAIv3qOy7K63mWoN15-MfA0Ke1Mc3Jh2KUiSXnNHaB60jwOvxCQiI2hMtLKvMhUNLRKXggHx-5NkXH-OSkjd7VAb1/http%3A%2F%2Fwww.isglobal.org%2F>.


CONFIDENCIALIDAD. Este mensaje y sus anexos se dirigen exclusivamente a
destinatario y puede contener informaci�n confidencial, por lo que la
divulgaci�n y/o copia sin autorizaci�n est� prohibida por la
vigente. Si ha recibido este mensaje por error, le rogamos lo
inmediatamente por esta misma v�a y proceda a su destrucci�n.

PROTECCI�N DE DATOS. Sus datos de car�cter personal utilizados en este
env�o, incluida su direcci�n de e-mail, forman parte de ficheros de
de la Fundaci�n ISGlobal  para cualquier
finalidades de
contacto, relaci�n institucional y/o env�o de informaci�n sobre
actividades. Los datos que usted nos pueda facilitar contestando este
correo quedar�n incorporados en los correspondientes ficheros, autorizando
uso de su direcci�n de e-mail para las finalidades citadas. Puede
ejercer los
derechos de acceso, rectificaci�n, cancelaci�n y oposici�n
dirigi�ndose a lopd using isglobal.org <mailto:lopd using isglobal.org>* *. Pol�tica de
en http://secure-web.cisco.com/1jYETCf8Z31mlXyEguj5N_4uRYqLgUzUHJ8zg3l8Y-HNg-qmPlR42_sLritOL8uyojzNYQSZAAQtaxkCs6Zab0JLnhS4uZ_cyP4punoMuz-iCONz0xcozMsaz0d1XhZammfouvRSiQ9TAU9YwRhn5wlQ2JqDvR5boanPU6LmqISZPQ2kpjK4w5yPnxjishrbMvR0ZZFavIjMOuYj4h9rY9TZy7ECyHkSfhIWv4O3PcPuVYoWnwBFeYxVeA_hTyxHFetioldkLbyONQFpUVpyPgXAHjZlKu0DZ-JQA_S_0vy3h_ge-6kgecwpGdaZgPd51/http%3A%2F%2Fwww.isglobal.org <http://secure-web.cisco.com/1IP90dh07vlVZJb49MNYD5PAAbqci8TPvWXhLl18hjJvjKc-W1tJ30bY5bAKRf0AFzly80g7KL4d-0DdDL6H9DW4uEr2GNgDAk_39Vt-l_nTM0a0bJIepy9MjxBHXbP42_XYLskYkz0jX62et39hHKTSj3jCrOHlcc2wTMyHUYA1C9YL9zgTy4Dv39In8duSS_QxXH2tAHEmjsyIBi9ue1V2Y7b2k8yMHUfRyDqFBAIv3qOy7K63mWoN15-MfA0Ke1Mc3Jh2KUiSXnNHaB60jwOvxCQiI2hMtLKvMhUNLRKXggHx-5NkXH-OSkjd7VAb1/http%3A%2F%2Fwww.isglobal.org%2F>.

        [[alternative HTML version deleted]]

Bioc-devel using r-project.org mailing list

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]]

More information about the Bioc-devel mailing list