Re: [Rd] could not find function after import
Duncan I have a related question. I need one function from R.utils. But R.utils depends on R.oo and R.methodsS3. so I made R.util an import and then used importFrom() in the namespace. The package passed the check. However when it came to use the function it had not been loaded? do I need to add the upstream packages that R.util depends upon? also in the code do I need a library or require? A bit confused Steve On Mon, Sep 19, 2011 at 5:09 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 11-09-19 4:48 PM, Stephanie M. Gogarten wrote: I am trying to build a package (GWASTools, submitted to Bioconductor) that uses the sandwich package. I have references to sandwich in DESCRIPTION: Imports: methods, DBI, RSQLite, sandwich, survival, DNAcopy and NAMESPACE: import(sandwich) In the code itself is a call to vcovHC: Vhat- vcovHC(mod, type=HC0) I have sandwich version 2.2-7 installed. When I run R CMD check on my package, I get the following error during checking of examples: * using R Under development (unstable) (2011-08-29 r56828) * using platform: x86_64-apple-darwin9.8.0 (64-bit) ... * checking examples ... ERROR ... Error in estfun.glm(x) : could not find function is.zoo Calls: assocTestRegression ... meatHC - rowMeans - is.data.frame - estfun - estfun.glm I import sandwich, sandwich depends on zoo, but a function in zoo cannot be found during execution. I tried to get around this by explicitly including a require statement in assocTestRegression: require(sandwich) The example now runs, but I have a warning in R CMD check: * checking for unstated dependencies in R code ... WARNING ‘library’ or ‘require’ call not declared from: ‘sandwich’ I am not sure why this is a problem, as there is a require statement (for a different package) in another function which does not cause any warnings. Can anyone advise on how to get my package to successfully pass R CMD check? If you said that your package Depends on sandwich, you'd probably pass checks, but this is arguably a bug in the sandwich package. The problem is that since you only import sandwich, it never gets attached. So it never attaches its dependency zoo. It should import zoo (or import the functions in zoo that it uses) to work properly the way you are calling it. You can see the same error as follows: 1. Install sandwich, but don't attach it or zoo. 2. Run example(glm) to create the glm object glm.D93. Try to call sandwich::estfun(glm.D93) You'll get the same error as before because is.zoo() will not be loaded. It's also arguably a design flaw in R. For testing sandwich, zoo would generally end up being attached, because the testing of sandwich would attach it. However, examples like the one above are never tested. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] could not find function after import
On 23/09/2011 12:57 PM, steven mosher wrote: Duncan I have a related question. I need one function from R.utils. But R.utils depends on R.oo and R.methodsS3. so I made R.util an import and then used importFrom() in the namespace. The package passed the check. However when it came to use the function it had not been loaded? do I need to add the upstream packages that R.util depends upon? also in the code do I need a library or require? Sounds exactly like the situation with sandwich below.The workaround available to you is to Depend on R.utils. The author of R.utils could fix the problem by importing R.oo and R.methodsS3, and the authors of R could fix it by changing the behaviour of how R handles imports. Duncan Murdoch A bit confused Steve On Mon, Sep 19, 2011 at 5:09 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 11-09-19 4:48 PM, Stephanie M. Gogarten wrote: I am trying to build a package (GWASTools, submitted to Bioconductor) that uses the sandwich package. I have references to sandwich in DESCRIPTION: Imports: methods, DBI, RSQLite, sandwich, survival, DNAcopy and NAMESPACE: import(sandwich) In the code itself is a call to vcovHC: Vhat- vcovHC(mod, type=HC0) I have sandwich version 2.2-7 installed. When I run R CMD check on my package, I get the following error during checking of examples: * using R Under development (unstable) (2011-08-29 r56828) * using platform: x86_64-apple-darwin9.8.0 (64-bit) ... * checking examples ... ERROR ... Error in estfun.glm(x) : could not find function is.zoo Calls: assocTestRegression ... meatHC -rowMeans -is.data.frame - estfun -estfun.glm I import sandwich, sandwich depends on zoo, but a function in zoo cannot be found during execution. I tried to get around this by explicitly including a require statement in assocTestRegression: require(sandwich) The example now runs, but I have a warning in R CMD check: * checking for unstated dependencies in R code ... WARNING ‘library’ or ‘require’ call not declared from: ‘sandwich’ I am not sure why this is a problem, as there is a require statement (for a different package) in another function which does not cause any warnings. Can anyone advise on how to get my package to successfully pass R CMD check? If you said that your package Depends on sandwich, you'd probably pass checks, but this is arguably a bug in the sandwich package. The problem is that since you only import sandwich, it never gets attached. So it never attaches its dependency zoo. It should import zoo (or import the functions in zoo that it uses) to work properly the way you are calling it. You can see the same error as follows: 1. Install sandwich, but don't attach it or zoo. 2. Run example(glm) to create the glm object glm.D93. Try to call sandwich::estfun(glm.D93) You'll get the same error as before because is.zoo() will not be loaded. It's also arguably a design flaw in R. For testing sandwich, zoo would generally end up being attached, because the testing of sandwich would attach it. However, examples like the one above are never tested. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] could not find function after import
Thanks duncan. I fixed it by changing to depends and resubmitting my packages. But I changed from depends to imports for a very specific reason. namespace conflicts. There are work arounds for that so its not terminally broken, but IMPORT had the promise of just the elegance I was looking for. Thanks for the explanation. Steve On Fri, Sep 23, 2011 at 11:44 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 23/09/2011 12:57 PM, steven mosher wrote: Duncan I have a related question. I need one function from R.utils. But R.utils depends on R.oo and R.methodsS3. so I made R.util an import and then used importFrom() in the namespace. The package passed the check. However when it came to use the function it had not been loaded? do I need to add the upstream packages that R.util depends upon? also in the code do I need a library or require? Sounds exactly like the situation with sandwich below. The workaround available to you is to Depend on R.utils. The author of R.utils could fix the problem by importing R.oo and R.methodsS3, and the authors of R could fix it by changing the behaviour of how R handles imports. Duncan Murdoch A bit confused Steve On Mon, Sep 19, 2011 at 5:09 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 11-09-19 4:48 PM, Stephanie M. Gogarten wrote: I am trying to build a package (GWASTools, submitted to Bioconductor) that uses the sandwich package. I have references to sandwich in DESCRIPTION: Imports: methods, DBI, RSQLite, sandwich, survival, DNAcopy and NAMESPACE: import(sandwich) In the code itself is a call to vcovHC: Vhat- vcovHC(mod, type=HC0) I have sandwich version 2.2-7 installed. When I run R CMD check on my package, I get the following error during checking of examples: * using R Under development (unstable) (2011-08-29 r56828) * using platform: x86_64-apple-darwin9.8.0 (64-bit) ... * checking examples ... ERROR ... Error in estfun.glm(x) : could not find function is.zoo Calls: assocTestRegression ... meatHC - rowMeans - is.data.frame - estfun - estfun.glm I import sandwich, sandwich depends on zoo, but a function in zoo cannot be found during execution. I tried to get around this by explicitly including a require statement in assocTestRegression: require(sandwich) The example now runs, but I have a warning in R CMD check: * checking for unstated dependencies in R code ... WARNING ‘library’ or ‘require’ call not declared from: ‘sandwich’ I am not sure why this is a problem, as there is a require statement (for a different package) in another function which does not cause any warnings. Can anyone advise on how to get my package to successfully pass R CMD check? If you said that your package Depends on sandwich, you'd probably pass checks, but this is arguably a bug in the sandwich package. The problem is that since you only import sandwich, it never gets attached. So it never attaches its dependency zoo. It should import zoo (or import the functions in zoo that it uses) to work properly the way you are calling it. You can see the same error as follows: 1. Install sandwich, but don't attach it or zoo. 2. Run example(glm) to create the glm object glm.D93. Try to call sandwich::estfun(glm.D93) You'll get the same error as before because is.zoo() will not be loaded. It's also arguably a design flaw in R. For testing sandwich, zoo would generally end up being attached, because the testing of sandwich would attach it. However, examples like the one above are never tested. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] could not find function after import
I am trying to build a package (GWASTools, submitted to Bioconductor) that uses the sandwich package. I have references to sandwich in DESCRIPTION: Imports: methods, DBI, RSQLite, sandwich, survival, DNAcopy and NAMESPACE: import(sandwich) In the code itself is a call to vcovHC: Vhat - vcovHC(mod, type=HC0) I have sandwich version 2.2-7 installed. When I run R CMD check on my package, I get the following error during checking of examples: * using R Under development (unstable) (2011-08-29 r56828) * using platform: x86_64-apple-darwin9.8.0 (64-bit) ... * checking examples ... ERROR ... Error in estfun.glm(x) : could not find function is.zoo Calls: assocTestRegression ... meatHC - rowMeans - is.data.frame - estfun - estfun.glm I import sandwich, sandwich depends on zoo, but a function in zoo cannot be found during execution. I tried to get around this by explicitly including a require statement in assocTestRegression: require(sandwich) The example now runs, but I have a warning in R CMD check: * checking for unstated dependencies in R code ... WARNING ‘library’ or ‘require’ call not declared from: ‘sandwich’ I am not sure why this is a problem, as there is a require statement (for a different package) in another function which does not cause any warnings. Can anyone advise on how to get my package to successfully pass R CMD check? thanks, Stephanie Gogarten Research Scientist, Biostatistics University of Washington __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] could not find function after import
On 11-09-19 4:48 PM, Stephanie M. Gogarten wrote: I am trying to build a package (GWASTools, submitted to Bioconductor) that uses the sandwich package. I have references to sandwich in DESCRIPTION: Imports: methods, DBI, RSQLite, sandwich, survival, DNAcopy and NAMESPACE: import(sandwich) In the code itself is a call to vcovHC: Vhat- vcovHC(mod, type=HC0) I have sandwich version 2.2-7 installed. When I run R CMD check on my package, I get the following error during checking of examples: * using R Under development (unstable) (2011-08-29 r56828) * using platform: x86_64-apple-darwin9.8.0 (64-bit) ... * checking examples ... ERROR ... Error in estfun.glm(x) : could not find function is.zoo Calls: assocTestRegression ... meatHC - rowMeans - is.data.frame - estfun - estfun.glm I import sandwich, sandwich depends on zoo, but a function in zoo cannot be found during execution. I tried to get around this by explicitly including a require statement in assocTestRegression: require(sandwich) The example now runs, but I have a warning in R CMD check: * checking for unstated dependencies in R code ... WARNING ‘library’ or ‘require’ call not declared from: ‘sandwich’ I am not sure why this is a problem, as there is a require statement (for a different package) in another function which does not cause any warnings. Can anyone advise on how to get my package to successfully pass R CMD check? If you said that your package Depends on sandwich, you'd probably pass checks, but this is arguably a bug in the sandwich package. The problem is that since you only import sandwich, it never gets attached. So it never attaches its dependency zoo. It should import zoo (or import the functions in zoo that it uses) to work properly the way you are calling it. You can see the same error as follows: 1. Install sandwich, but don't attach it or zoo. 2. Run example(glm) to create the glm object glm.D93. Try to call sandwich::estfun(glm.D93) You'll get the same error as before because is.zoo() will not be loaded. It's also arguably a design flaw in R. For testing sandwich, zoo would generally end up being attached, because the testing of sandwich would attach it. However, examples like the one above are never tested. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
