snapCGH: T instead of TRUE, etc
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Ramon Diaz ★ 1.1k
@ramon-diaz-159
Last seen 9.6 years ago
Dear All, Somewhat similar to what I reported before, with snapCGH I am getting errors, when building a package, that can be traced to errors in snapCGH. Specifically: The functions "find.param.{two.three..}" lead to errors such as Error in matrix(c(1 - p1, p1, p2, 1 - p2), ncol = 2, b = T) : T used instead of TRUE Error in matrix(c(1 - p1, p1, p2, 1 - p2), ncol = 2, b = T) : recursive default argument reference And the functions Viterbi.{two.three..} also show similar problems, as in Error in matrix(nrow = K, ncol = n, b = T) : T used instead of TRUE Error in matrix(nrow = K, ncol = n, b = T) : recursive default argument referenc max(-1e+05, log(BFGS.output$prior[i]), na.rm = T) T used instead of TRUE Once all the appropriate T are replaced by TRUE things are OK again. Best, R. -- Ram?n D?az-Uriarte Statistical Computing Team Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://ligarto.org/rdiaz PGP KeyID: 0xE89B3462 (http://ligarto.org/rdiaz/0xE89B3462.asc) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en s...{{dropped}}
Cancer snapCGH Cancer snapCGH • 1.2k views
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Ramon Diaz ★ 1.1k
@ramon-diaz-159
Last seen 9.6 years ago
Sorry, I forgot to say I am seeing this with versions 1.2.0 (BioC 1.9) and 1.3.2 (BioC 2.0) of snapCGH (R-2.4., under Debian GNU/Linux). R. On Friday 16 March 2007 14:29, Ramon Diaz-Uriarte wrote: > Dear All, > > Somewhat similar to what I reported before, with snapCGH I am getting > errors, when building a package, that can be traced to errors in snapCGH. > Specifically: > > The functions "find.param.{two.three..}" lead to errors such as > > Error in matrix(c(1 - p1, p1, p2, 1 - p2), ncol = 2, b = T) : > T used instead of TRUE > Error in matrix(c(1 - p1, p1, p2, 1 - p2), ncol = 2, b = T) : > recursive default argument reference > > > > > And the functions Viterbi.{two.three..} also show similar problems, as in > > Error in matrix(nrow = K, ncol = n, b = T) : > T used instead of TRUE > Error in matrix(nrow = K, ncol = n, b = T) : > recursive default argument referenc > > max(-1e+05, log(BFGS.output$prior[i]), na.rm = T) > T used instead of TRUE > > > > > Once all the appropriate T are replaced by TRUE things are OK again. > > > > Best, > > > R. -- Ram?n D?az-Uriarte Statistical Computing Team Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://ligarto.org/rdiaz PGP KeyID: 0xE89B3462 (http://ligarto.org/rdiaz/0xE89B3462.asc) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en s...{{dropped}}
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Hi Ramon, I've made and uploaded the changes you suggested. All instances of T have been changed to TRUE in the appropriate source files. It's not an issue I've ever seen before. Mike Smith Quoting Ramon Diaz-Uriarte <rdiaz at="" cnio.es="">: > Sorry, I forgot to say I am seeing this with versions 1.2.0 (BioC 1.9) and > 1.3.2 (BioC 2.0) of snapCGH (R-2.4., under Debian GNU/Linux). > > R. > > On Friday 16 March 2007 14:29, Ramon Diaz-Uriarte wrote: >> Dear All, >> >> Somewhat similar to what I reported before, with snapCGH I am getting >> errors, when building a package, that can be traced to errors in snapCGH. >> Specifically: >> >> The functions "find.param.{two.three..}" lead to errors such as >> >> Error in matrix(c(1 - p1, p1, p2, 1 - p2), ncol = 2, b = T) : >> T used instead of TRUE >> Error in matrix(c(1 - p1, p1, p2, 1 - p2), ncol = 2, b = T) : >> recursive default argument reference >> >> >> >> >> And the functions Viterbi.{two.three..} also show similar problems, as in >> >> Error in matrix(nrow = K, ncol = n, b = T) : >> T used instead of TRUE >> Error in matrix(nrow = K, ncol = n, b = T) : >> recursive default argument referenc >> >> max(-1e+05, log(BFGS.output$prior[i]), na.rm = T) >> T used instead of TRUE >> >> >> >> >> Once all the appropriate T are replaced by TRUE things are OK again. >> >> >> >> Best, >> >> >> R. > > -- > Ram?n D?az-Uriarte > Statistical Computing Team > Centro Nacional de Investigaciones Oncol?gicas (CNIO) > (Spanish National Cancer Center) > Melchor Fern?ndez Almagro, 3 > 28029 Madrid (Spain) > Fax: +-34-91-224-6972 > Phone: +-34-91-224-6900 > > http://ligarto.org/rdiaz > PGP KeyID: 0xE89B3462 > (http://ligarto.org/rdiaz/0xE89B3462.asc) > > > > **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en s...{{dropped}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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On Friday 16 March 2007 17:41, ma3mls at bath.ac.uk wrote: > Hi Ramon, > > I've made and uploaded the changes you suggested. All instances of T > have been changed to TRUE in the appropriate source files. > > It's not an issue I've ever seen before. > Thanks Mike! Actually, I was quite surprised because it does not show up in interactive usage, only while doing an R CMD check of a package that uses the non-homogeneous HMM functions. Best, R. > Mike Smith > > Quoting Ramon Diaz-Uriarte <rdiaz at="" cnio.es="">: > > Sorry, I forgot to say I am seeing this with versions 1.2.0 (BioC 1.9) > > and 1.3.2 (BioC 2.0) of snapCGH (R-2.4., under Debian GNU/Linux). > > > > R. > > > > On Friday 16 March 2007 14:29, Ramon Diaz-Uriarte wrote: > >> Dear All, > >> > >> Somewhat similar to what I reported before, with snapCGH I am getting > >> errors, when building a package, that can be traced to errors in > >> snapCGH. Specifically: > >> > >> The functions "find.param.{two.three..}" lead to errors such as > >> > >> Error in matrix(c(1 - p1, p1, p2, 1 - p2), ncol = 2, b = T) : > >> T used instead of TRUE > >> Error in matrix(c(1 - p1, p1, p2, 1 - p2), ncol = 2, b = T) : > >> recursive default argument reference > >> > >> > >> > >> > >> And the functions Viterbi.{two.three..} also show similar problems, as > >> in > >> > >> Error in matrix(nrow = K, ncol = n, b = T) : > >> T used instead of TRUE > >> Error in matrix(nrow = K, ncol = n, b = T) : > >> recursive default argument referenc > >> > >> max(-1e+05, log(BFGS.output$prior[i]), na.rm = T) > >> T used instead of TRUE > >> > >> > >> > >> > >> Once all the appropriate T are replaced by TRUE things are OK again. > >> > >> > >> > >> Best, > >> > >> > >> R. > > > > -- > > Ram?n D?az-Uriarte > > Statistical Computing Team > > Centro Nacional de Investigaciones Oncol?gicas (CNIO) > > (Spanish National Cancer Center) > > Melchor Fern?ndez Almagro, 3 > > 28029 Madrid (Spain) > > Fax: +-34-91-224-6972 > > Phone: +-34-91-224-6900 > > > > http://ligarto.org/rdiaz > > PGP KeyID: 0xE89B3462 > > (http://ligarto.org/rdiaz/0xE89B3462.asc) > > > > > > > > **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en > > s...{{dropped}} > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Ram?n D?az-Uriarte Statistical Computing Team Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://ligarto.org/rdiaz PGP KeyID: 0xE89B3462 (http://ligarto.org/rdiaz/0xE89B3462.asc) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en s...{{dropped}}
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