Re: [Bioc-devel] PROTECT errors in Bioconductor packages
> The tool is not perfect, so assess each report carefully. I also get a warning on almost every C++ function I've written, because I use the following code to handle exceptions: SEXP output=PROTECT(allocVector(...)); try { // do something that might raise an exception } catch (std::exception& e) { UNPROTECT(1); throw; // break out of this part of the function } UNPROTECT(1); return output; Presumably the check doesn't account for transfer of control to the catch block. I find that R itself is pretty good at complaining about stack imbalances during execution of tests, examples, etc. > 'My' packages > (Rsamtools, DirichletMultinomial) had several false positives (all > associated with use of an attribute of a protected SEXP), one subtle > problem (a symbol from a PROTECT'ed package name space; the symbol could > in theory be an active binding and the value obtained not PROTECTed by > the name space), and a genuine bug > > tag = NEW_CHARACTER(n); > for (int j = 0; j < n; ++j) > SET_STRING_ELT(tag, j, NA_STRING); > if ('A' == aux[0]) { > buf_A = R_alloc(2, sizeof(char)); # <<- bug > buf_A[1] = '\0'; > } > ... > SET_VECTOR_ELT(tags, i, tag); # PROTECT tag, too late! I assume the bug refers to the un-PROTECT'd NEW_CHARACTER here - the R_alloc call looks okay to me... Cheers, Aaron ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] PROTECT errors in Bioconductor packages
On 04/06/2017 05:33 AM, Aaron Lun wrote: The tool is not perfect, so assess each report carefully. I also get a warning on almost every C++ function I've written, because I use the following code to handle exceptions: SEXP output=PROTECT(allocVector(...)); try { // do something that might raise an exception } catch (std::exception& e) { UNPROTECT(1); throw; // break out of this part of the function } UNPROTECT(1); return output; Presumably the check doesn't account for transfer of control to the catch block. I find that R itself is pretty good at complaining about stack imbalances during execution of tests, examples, etc. 'My' packages (Rsamtools, DirichletMultinomial) had several false positives (all associated with use of an attribute of a protected SEXP), one subtle problem (a symbol from a PROTECT'ed package name space; the symbol could in theory be an active binding and the value obtained not PROTECTed by the name space), and a genuine bug tag = NEW_CHARACTER(n); for (int j = 0; j < n; ++j) SET_STRING_ELT(tag, j, NA_STRING); if ('A' == aux[0]) { buf_A = R_alloc(2, sizeof(char)); # <<- bug buf_A[1] = '\0'; } ... SET_VECTOR_ELT(tags, i, tag); # PROTECT tag, too late! I assume the bug refers to the un-PROTECT'd NEW_CHARACTER here - the R_alloc call looks okay to me... yes, tag needs protection. I attributed the bug to R_alloc because I failed to reason that R_alloc (obviously) allocates and hence can trigger a garbage collection. Somehow it reflects my approach to PROTECTion, probably not shared by everyone. I like to PROTECT only when necessary, rather than indiscriminately. Probably this has no practical consequence in terms of performance, making the code a little easier to read at the expense of exposing me to bugs like this. Martin Cheers, Aaron ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or...{{dropped:2}} ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] PROTECT errors in Bioconductor packages
On Thu, Apr 6, 2017 at 2:59 AM, Martin Morgan wrote: > On 04/06/2017 05:33 AM, Aaron Lun wrote: >>> >>> The tool is not perfect, so assess each report carefully. >> >> >> I also get a warning on almost every C++ function I've written, because >> I use the following code to handle exceptions: >> >> SEXP output=PROTECT(allocVector(...)); >> try { >> // do something that might raise an exception >> } catch (std::exception& e) { >> UNPROTECT(1); >> throw; // break out of this part of the function >> } >> UNPROTECT(1); >> return output; >> >> Presumably the check doesn't account for transfer of control to the >> catch block. I find that R itself is pretty good at complaining about >> stack imbalances during execution of tests, examples, etc. >> >>> 'My' packages >>> (Rsamtools, DirichletMultinomial) had several false positives (all >>> associated with use of an attribute of a protected SEXP), one subtle >>> problem (a symbol from a PROTECT'ed package name space; the symbol could >>> in theory be an active binding and the value obtained not PROTECTed by >>> the name space), and a genuine bug >>> >>> tag = NEW_CHARACTER(n); >>> for (int j = 0; j < n; ++j) >>> SET_STRING_ELT(tag, j, NA_STRING); >>> if ('A' == aux[0]) { >>> buf_A = R_alloc(2, sizeof(char)); # <<- bug >>> buf_A[1] = '\0'; >>> } >>> ... >>> SET_VECTOR_ELT(tags, i, tag); # PROTECT tag, too late! >> >> >> I assume the bug refers to the un-PROTECT'd NEW_CHARACTER here - the >> R_alloc call looks okay to me... > > > yes, tag needs protection. > > I attributed the bug to R_alloc because I failed to reason that R_alloc > (obviously) allocates and hence can trigger a garbage collection. > > Somehow it reflects my approach to PROTECTion, probably not shared by > everyone. I like to PROTECT only when necessary, rather than > indiscriminately. Probably this has no practical consequence in terms of > performance, making the code a little easier to read at the expense of > exposing me to bugs like this. > I guess it's a tradeoff between syntactic complexity and logical complexity. You have to think pretty hard to minimize use of the protect stack. One recommendation might be to UNPROTECT() as soon as the pointer on the top is unneeded, rather than trying to figure out the number to pop just before returning to R. One thing that got me is that the order in which C evaluates function call arguments is undefined. I did a lot of R_setAttrib(x, install("foo"), allocBar()), thinking that the symbol would be automatically protected, and allocBar() would not need protection, since it happened last. Unfortunately, it might be evaluated first. Btw, I think my package RGtk2 got the record: 1952 errors. Luckily almost all of them happened inside a few macros and autogenerated code. > Martin > >> >> Cheers, >> >> Aaron >> ___ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > > This email message may contain legally privileged and/or...{{dropped:2}} > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] PROTECT errors in Bioconductor packages
On 04/06/2017 03:29 AM, Michael Lawrence wrote: On Thu, Apr 6, 2017 at 2:59 AM, Martin Morgan wrote: On 04/06/2017 05:33 AM, Aaron Lun wrote: The tool is not perfect, so assess each report carefully. I get a lot of warnings because the tool seems to consider that extracting an attribute (with getAttrib(x, ...)) or extracting the slot of an S4 object (with GET_SLOT(x, ...) or R_do_slot(x, ...)) returns an SEXP that needs protection. I always assumed that it didn't because my understanding is that the returned SEXP is pointing to a part of a pre-existing object ('x') and not to a newly created one. So I decided I could treat it like the SEXP returned by VECTOR_ELT(), which, AFAIK, doesn't need protection. So I suspect these warnings are false positives but I'm not 100% sure. I also get a warning on almost every C++ function I've written, because I use the following code to handle exceptions: SEXP output=PROTECT(allocVector(...)); try { // do something that might raise an exception } catch (std::exception& e) { UNPROTECT(1); throw; // break out of this part of the function } UNPROTECT(1); return output; Presumably the check doesn't account for transfer of control to the catch block. I find that R itself is pretty good at complaining about stack imbalances during execution of tests, examples, etc. 'My' packages (Rsamtools, DirichletMultinomial) had several false positives (all associated with use of an attribute of a protected SEXP), one subtle problem (a symbol from a PROTECT'ed package name space; the symbol could in theory be an active binding and the value obtained not PROTECTed by the name space), and a genuine bug tag = NEW_CHARACTER(n); for (int j = 0; j < n; ++j) SET_STRING_ELT(tag, j, NA_STRING); if ('A' == aux[0]) { buf_A = R_alloc(2, sizeof(char)); # <<- bug buf_A[1] = '\0'; } ... SET_VECTOR_ELT(tags, i, tag); # PROTECT tag, too late! I assume the bug refers to the un-PROTECT'd NEW_CHARACTER here - the R_alloc call looks okay to me... yes, tag needs protection. I attributed the bug to R_alloc because I failed to reason that R_alloc (obviously) allocates and hence can trigger a garbage collection. Somehow it reflects my approach to PROTECTion, probably not shared by everyone. I like to PROTECT only when necessary, rather than indiscriminately. Probably this has no practical consequence in terms of performance, making the code a little easier to read at the expense of exposing me to bugs like this. I guess it's a tradeoff between syntactic complexity and logical complexity. You have to think pretty hard to minimize use of the protect stack. I prefer to call it logical obscurity ;-) The hard thinking consists in assessing whether or not the code between the line where a new SEXP is allocated (line X) and the line where it's put in a safe place (line Y) can trigger garbage collection. Hard to figure out in general indeed, but not impossible! Problem is that the result of this assessment is valid at a certain point in time but might change in the future, even if your code has not changed. So a dangerous game for virtually zero benefits. One recommendation might be to UNPROTECT() as soon as the pointer on the top is unneeded, rather than trying to figure out the number to pop just before returning to R. If you PROTECT() in a loop, you definitely want to do that. Otherwise, does it make a big difference? One thing that got me is that the order in which C evaluates function call arguments is undefined. I did a lot of R_setAttrib(x, install("foo"), allocBar()), thinking that the symbol would be automatically protected, and allocBar() would not need protection, since it happened last. Unfortunately, it might be evaluated first. I got hit by this too long time ago but with defineVar() instead of R_setAttrib(): https://stat.ethz.ch/pipermail/r-devel/2008-January/048040.html H. Btw, I think my package RGtk2 got the record: 1952 errors. Luckily almost all of them happened inside a few macros and autogenerated code. Martin Cheers, Aaron ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=su20YzStywMa_pdWblzF0RnK8ATRw-t61lOIOsi0xTU&s=JhBOw1ac5wXfV1BSjFuidxFiBTx43J7iEvZG4G0_0uU&e= This email message may contain legally privileged and/or...{{dropped:2}} ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=su20YzStywMa_pdWblzF0RnK8AT
Re: [Bioc-devel] PROTECT errors in Bioconductor packages
On Fri, 7 Apr 2017, Hervé Pagès wrote: On 04/06/2017 03:29 AM, Michael Lawrence wrote: On Thu, Apr 6, 2017 at 2:59 AM, Martin Morgan wrote: On 04/06/2017 05:33 AM, Aaron Lun wrote: The tool is not perfect, so assess each report carefully. I get a lot of warnings because the tool seems to consider that extracting an attribute (with getAttrib(x, ...)) or extracting the slot of an S4 object (with GET_SLOT(x, ...) or R_do_slot(x, ...)) returns an SEXP that needs protection. I always assumed that it didn't because my understanding is that the returned SEXP is pointing to a part of a pre-existing object ('x') and not to a newly created one. So I decided I could treat it like the SEXP returned by VECTOR_ELT(), which, AFAIK, doesn't need protection. So I suspect these warnings are false positives but I'm not 100% sure. If you are not 100% sure then you should protect :-) There are some cases, in particular related to compact row names on data frames, where getAttrib will allocate. Best, luke I also get a warning on almost every C++ function I've written, because I use the following code to handle exceptions: SEXP output=PROTECT(allocVector(...)); try { // do something that might raise an exception } catch (std::exception& e) { UNPROTECT(1); throw; // break out of this part of the function } UNPROTECT(1); return output; Presumably the check doesn't account for transfer of control to the catch block. I find that R itself is pretty good at complaining about stack imbalances during execution of tests, examples, etc. 'My' packages (Rsamtools, DirichletMultinomial) had several false positives (all associated with use of an attribute of a protected SEXP), one subtle problem (a symbol from a PROTECT'ed package name space; the symbol could in theory be an active binding and the value obtained not PROTECTed by the name space), and a genuine bug tag = NEW_CHARACTER(n); for (int j = 0; j < n; ++j) SET_STRING_ELT(tag, j, NA_STRING); if ('A' == aux[0]) { buf_A = R_alloc(2, sizeof(char)); # <<- bug buf_A[1] = '\0'; } ... SET_VECTOR_ELT(tags, i, tag); # PROTECT tag, too late! I assume the bug refers to the un-PROTECT'd NEW_CHARACTER here - the R_alloc call looks okay to me... yes, tag needs protection. I attributed the bug to R_alloc because I failed to reason that R_alloc (obviously) allocates and hence can trigger a garbage collection. Somehow it reflects my approach to PROTECTion, probably not shared by everyone. I like to PROTECT only when necessary, rather than indiscriminately. Probably this has no practical consequence in terms of performance, making the code a little easier to read at the expense of exposing me to bugs like this. I guess it's a tradeoff between syntactic complexity and logical complexity. You have to think pretty hard to minimize use of the protect stack. I prefer to call it logical obscurity ;-) The hard thinking consists in assessing whether or not the code between the line where a new SEXP is allocated (line X) and the line where it's put in a safe place (line Y) can trigger garbage collection. Hard to figure out in general indeed, but not impossible! Problem is that the result of this assessment is valid at a certain point in time but might change in the future, even if your code has not changed. So a dangerous game for virtually zero benefits. One recommendation might be to UNPROTECT() as soon as the pointer on the top is unneeded, rather than trying to figure out the number to pop just before returning to R. If you PROTECT() in a loop, you definitely want to do that. Otherwise, does it make a big difference? One thing that got me is that the order in which C evaluates function call arguments is undefined. I did a lot of R_setAttrib(x, install("foo"), allocBar()), thinking that the symbol would be automatically protected, and allocBar() would not need protection, since it happened last. Unfortunately, it might be evaluated first. I got hit by this too long time ago but with defineVar() instead of R_setAttrib(): https://stat.ethz.ch/pipermail/r-devel/2008-January/048040.html H. Btw, I think my package RGtk2 got the record: 1952 errors. Luckily almost all of them happened inside a few macros and autogenerated code. Martin Cheers, Aaron ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=su20YzStywMa_pdWblzF0RnK8ATRw-t61lOIOsi0xTU&s=JhBOw1ac5wXfV1BSjFuidxFiBTx43J7iEvZG4G0_0uU&e= This email message may contain legally privileged and/or...{{dropped:2}} ___ Bioc-devel@r-project
Re: [Bioc-devel] PROTECT errors in Bioconductor packages
On 04/07/2017 05:37 AM, luke-tier...@uiowa.edu wrote: On Fri, 7 Apr 2017, Hervé Pagès wrote: On 04/06/2017 03:29 AM, Michael Lawrence wrote: On Thu, Apr 6, 2017 at 2:59 AM, Martin Morgan wrote: On 04/06/2017 05:33 AM, Aaron Lun wrote: The tool is not perfect, so assess each report carefully. I get a lot of warnings because the tool seems to consider that extracting an attribute (with getAttrib(x, ...)) or extracting the slot of an S4 object (with GET_SLOT(x, ...) or R_do_slot(x, ...)) returns an SEXP that needs protection. I always assumed that it didn't because my understanding is that the returned SEXP is pointing to a part of a pre-existing object ('x') and not to a newly created one. So I decided I could treat it like the SEXP returned by VECTOR_ELT(), which, AFAIK, doesn't need protection. So I suspect these warnings are false positives but I'm not 100% sure. If you are not 100% sure then you should protect :-) There are some cases, in particular related to compact row names on data frames, where getAttrib will allocate. Seriously? So setAttrib(x, ..., getAttrib) is not going to be a no-op anymore? Should I worry that VECTOR_ELT() will also expand some sort of compact list element? Why not keep these things low-level getters/setters that return whatever the real thing is and use higher-level accessors for returning the expanded version of the thing? Thanks, H. Best, luke I also get a warning on almost every C++ function I've written, because I use the following code to handle exceptions: SEXP output=PROTECT(allocVector(...)); try { // do something that might raise an exception } catch (std::exception& e) { UNPROTECT(1); throw; // break out of this part of the function } UNPROTECT(1); return output; Presumably the check doesn't account for transfer of control to the catch block. I find that R itself is pretty good at complaining about stack imbalances during execution of tests, examples, etc. 'My' packages (Rsamtools, DirichletMultinomial) had several false positives (all associated with use of an attribute of a protected SEXP), one subtle problem (a symbol from a PROTECT'ed package name space; the symbol could in theory be an active binding and the value obtained not PROTECTed by the name space), and a genuine bug tag = NEW_CHARACTER(n); for (int j = 0; j < n; ++j) SET_STRING_ELT(tag, j, NA_STRING); if ('A' == aux[0]) { buf_A = R_alloc(2, sizeof(char)); # <<- bug buf_A[1] = '\0'; } ... SET_VECTOR_ELT(tags, i, tag); # PROTECT tag, too late! I assume the bug refers to the un-PROTECT'd NEW_CHARACTER here - the R_alloc call looks okay to me... yes, tag needs protection. I attributed the bug to R_alloc because I failed to reason that R_alloc (obviously) allocates and hence can trigger a garbage collection. Somehow it reflects my approach to PROTECTion, probably not shared by everyone. I like to PROTECT only when necessary, rather than indiscriminately. Probably this has no practical consequence in terms of performance, making the code a little easier to read at the expense of exposing me to bugs like this. I guess it's a tradeoff between syntactic complexity and logical complexity. You have to think pretty hard to minimize use of the protect stack. I prefer to call it logical obscurity ;-) The hard thinking consists in assessing whether or not the code between the line where a new SEXP is allocated (line X) and the line where it's put in a safe place (line Y) can trigger garbage collection. Hard to figure out in general indeed, but not impossible! Problem is that the result of this assessment is valid at a certain point in time but might change in the future, even if your code has not changed. So a dangerous game for virtually zero benefits. One recommendation might be to UNPROTECT() as soon as the pointer on the top is unneeded, rather than trying to figure out the number to pop just before returning to R. If you PROTECT() in a loop, you definitely want to do that. Otherwise, does it make a big difference? One thing that got me is that the order in which C evaluates function call arguments is undefined. I did a lot of R_setAttrib(x, install("foo"), allocBar()), thinking that the symbol would be automatically protected, and allocBar() would not need protection, since it happened last. Unfortunately, it might be evaluated first. I got hit by this too long time ago but with defineVar() instead of R_setAttrib(): https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_r-2Ddevel_2008-2DJanuary_048040.html&d=DwID-g&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FscW1HcPCwUqtMwKVFDfd1NyW0oHh0tJOPdFb3C1IWk&s=O3CcB-Z_OkVKaC1aV0aIc5SCDNqGQrkvGSmPf0TRAsw&e= H. Btw, I think my package RGtk2 got the
Re: [Bioc-devel] PROTECT errors in Bioconductor packages
On Fri, 7 Apr 2017, Hervé Pagès wrote: On 04/07/2017 05:37 AM, luke-tier...@uiowa.edu wrote: On Fri, 7 Apr 2017, Hervé Pagès wrote: > On 04/06/2017 03:29 AM, Michael Lawrence wrote: > > On Thu, Apr 6, 2017 at 2:59 AM, Martin Morgan > > wrote: > > > On 04/06/2017 05:33 AM, Aaron Lun wrote: > > > > > > > > > > The tool is not perfect, so assess each report carefully. > > I get a lot of warnings because the tool seems to consider that > extracting an attribute (with getAttrib(x, ...)) or extracting the > slot of an S4 object (with GET_SLOT(x, ...) or R_do_slot(x, ...)) > returns an SEXP that needs protection. I always assumed that it > didn't because my understanding is that the returned SEXP is pointing > to a part of a pre-existing object ('x') and not to a newly created > one. So I decided I could treat it like the SEXP returned by > VECTOR_ELT(), which, AFAIK, doesn't need protection. > > So I suspect these warnings are false positives but I'm not 100% sure. If you are not 100% sure then you should protect :-) There are some cases, in particular related to compact row names on data frames, where getAttrib will allocate. Seriously? So setAttrib(x, ..., getAttrib) is not going to be a no-op anymore? Should I worry that VECTOR_ELT() will also expand some sort of compact list element? Why not keep these things low-level getters/setters that return whatever the real thing is and use higher-level accessors for returning the expanded version of the thing? Seriously: it's been that way since r37807 in 2006. If you want to read about some related future directions you can look at https://svn.r-project.org/R/branches/ALTREP/ALTREP.html. luke Thanks, H. Best, luke > > > > > > > > > > > > > I also get a warning on almost every C++ function I've written, > > > > because > > > > I use the following code to handle exceptions: > > > > > > > > SEXP output=PROTECT(allocVector(...)); > > > > try { > > > > // do something that might raise an exception > > > > } catch (std::exception& e) { > > > > UNPROTECT(1); > > > > throw; // break out of this part of the function > > > > } > > > > UNPROTECT(1); > > > > return output; > > > > > > > > Presumably the check doesn't account for transfer of control to > > > > the > > > > catch block. I find that R itself is pretty good at complaining > > > > about > > > > stack imbalances during execution of tests, examples, etc. > > > > > > > > > 'My' packages > > > > > (Rsamtools, DirichletMultinomial) had several false positives > > > > > (all > > > > > associated with use of an attribute of a protected SEXP), one > > > > > subtle > > > > > problem (a symbol from a PROTECT'ed package name space; the > > > > > symbol > > > > > could > > > > > in theory be an active binding and the value obtained not > > > > > PROTECTed by > > > > > the name space), and a genuine bug > > > > > > > > > > tag = NEW_CHARACTER(n); > > > > > for (int j = 0; j < n; ++j) > > > > > SET_STRING_ELT(tag, j, NA_STRING); > > > > > if ('A' == aux[0]) { > > > > > buf_A = R_alloc(2, sizeof(char)); # <<- bug > > > > > buf_A[1] = '\0'; > > > > > } > > > > > ... > > > > > SET_VECTOR_ELT(tags, i, tag); # PROTECT tag, too > > > > > late! > > > > > > > > > > > > I assume the bug refers to the un-PROTECT'd NEW_CHARACTER here - > > > > the > > > > R_alloc call looks okay to me... > > > > > > > > > yes, tag needs protection. > > > > > > I attributed the bug to R_alloc because I failed to reason that > > > R_alloc > > > (obviously) allocates and hence can trigger a garbage collection. > > > > > > Somehow it reflects my approach to PROTECTion, probably not shared > > > by > > > everyone. I like to PROTECT only when necessary, rather than > > > indiscriminately. Probably this has no practical consequence in > > > terms of > > > performance, making the code a little easier to read at the expense > > > of > > > exposing me to bugs like this. > > > > > > > I guess it's a tradeoff between syntactic complexity and logical > > complexity. You have to think pretty hard to minimize use of the > > protect stack. > > I prefer to call it logical obscurity ;-) > > The hard thinking consists in assessing whether or not the code between > the line where a new SEXP is allocated (line X) and the line where > it's put in a safe place (line Y) can trigger garbage collection. > Hard to figure out in general indeed, but not impossible! Problem > is that the result of this assessment is valid at a certain point > in time but might change in the future, even if your code has not > changed. > > So a dangerous game for virtually zero benefits. > > > > > One recommendation might be to UNPROTECT() as s
Re: [Bioc-devel] PROTECT errors in Bioconductor packages
On Fri, Apr 7, 2017 at 12:46 PM, wrote: > On Fri, 7 Apr 2017, Hervé Pagès wrote: > > On 04/07/2017 05:37 AM, luke-tier...@uiowa.edu wrote: >> >>> On Fri, 7 Apr 2017, Hervé Pagès wrote: >>> >>> > On 04/06/2017 03:29 AM, Michael Lawrence wrote: >>> > > On Thu, Apr 6, 2017 at 2:59 AM, Martin Morgan >>> > > wrote: >>> > > > On 04/06/2017 05:33 AM, Aaron Lun wrote: >>> > > > > > > > > > > The tool is not perfect, so assess each report >>> carefully. >>> > > I get a lot of warnings because the tool seems to consider that >>> > extracting an attribute (with getAttrib(x, ...)) or extracting the >>> > slot of an S4 object (with GET_SLOT(x, ...) or R_do_slot(x, ...)) >>> > returns an SEXP that needs protection. I always assumed that it >>> > didn't because my understanding is that the returned SEXP is pointing >>> > to a part of a pre-existing object ('x') and not to a newly created >>> > one. So I decided I could treat it like the SEXP returned by >>> > VECTOR_ELT(), which, AFAIK, doesn't need protection. >>> > > So I suspect these warnings are false positives but I'm not 100% >>> sure. >>> >>> If you are not 100% sure then you should protect :-) >>> >>> There are some cases, in particular related to compact row names on >>> data frames, where getAttrib will allocate. >>> >> >> Seriously? So setAttrib(x, ..., getAttrib) is not going to be a no-op >> anymore? Should I worry that VECTOR_ELT() will also expand some sort >> of compact list element? Why not keep these things low-level >> getters/setters that return whatever the real thing is and use >> higher-level accessors for returning the expanded version of the thing? >> > > Seriously: it's been that way since r37807 in 2006. > > If you want to read about some related future directions you can look at > https://svn.r-project.org/R/branches/ALTREP/ALTREP.html. Indeed. I was wondering whether to bring this up here. In a (hopefully near future) version of R-devel, doing, e.g., INTEGER(x) could allocate. There is a way to ask it to give you NULL instead of allocating if it would need to, but the point being it's probably going to get much harder to safely be clever about avoiding PROTECT'ing. (Luke put in temporary suspension of GC in some places, but I don't recall the exact details of where that was used). As a side note to the above, you'll need to do INTEGER(x) less often than you did before. There will be a new INTEGER_ELT and INTEGER_GET_REGION macros which (I think) will be guaranteed to not cause SEXP allocation. In terms of why, at least in the ALTREP case, it's so that these things can be passed directly to the R internals and be treated like whatever lowl-level type of thing they are (e.g. numeric vector, string vector, list, etc). This seamless backwards compatiblity requires that code which doesn't use the INTEGER_ELT and INTEGER_GET_REGION (or analogues) macros needs to have INTEGER(X) work and give it the pointer it expects, which won't necessarily exist before the first time it is required. Best, ~G > > luke > > > > >> Thanks, >> H. >> >> >>> Best, >>> >>> luke >>> >>> > > > > > > > > > > > > > I also get a warning on almost every C++ >>> function I've written, >>> > > > > because >>> > > > > I use the following code to handle exceptions: >>> > > > > > > > > SEXP output=PROTECT(allocVector(...)); >>> > > > > try { >>> > > > > // do something that might raise an exception >>> > > > > } catch (std::exception& e) { >>> > > > > UNPROTECT(1); >>> > > > > throw; // break out of this part of the function >>> > > > > } >>> > > > > UNPROTECT(1); >>> > > > > return output; >>> > > > > > > > > Presumably the check doesn't account for transfer of >>> control to > > > > the >>> > > > > catch block. I find that R itself is pretty good at complaining >>> > > > > about >>> > > > > stack imbalances during execution of tests, examples, etc. >>> > > > > > > > > > 'My' packages >>> > > > > > (Rsamtools, DirichletMultinomial) had several false positives >>> > > > > > (all >>> > > > > > associated with use of an attribute of a protected SEXP), one >>> > > > > > subtle >>> > > > > > problem (a symbol from a PROTECT'ed package name space; the > >>> > > > > symbol >>> > > > > > could >>> > > > > > in theory be an active binding and the value obtained not >>> > > > > > PROTECTed by >>> > > > > > the name space), and a genuine bug >>> > > > > > > > > > > tag = NEW_CHARACTER(n); >>> > > > > > for (int j = 0; j < n; ++j) >>> > > > > > SET_STRING_ELT(tag, j, NA_STRING); >>> > > > > > if ('A' == aux[0]) { >>> > > > > > buf_A = R_alloc(2, sizeof(char)); # <<- >>> bug >>> > > > > > buf_A[1] = '\0'; >>> > > > > > } >>> > > > > > ... >>> > > > > > SET_VECTOR_ELT(tags, i, tag); # PROTECT tag, >>> too >>> > > >
Re: [Bioc-devel] PROTECT errors in Bioconductor packages
On 07/04/17 20:46, luke-tier...@uiowa.edu wrote: > On Fri, 7 Apr 2017, Hervé Pagès wrote: > >> On 04/07/2017 05:37 AM, luke-tier...@uiowa.edu wrote: >>> On Fri, 7 Apr 2017, Hervé Pagès wrote: >>> >>> > On 04/06/2017 03:29 AM, Michael Lawrence wrote: >>> > > On Thu, Apr 6, 2017 at 2:59 AM, Martin Morgan >>> > > wrote: >>> > > > On 04/06/2017 05:33 AM, Aaron Lun wrote: >>> > > > > > > > > > > The tool is not perfect, so assess each report >>> carefully. >>> > > I get a lot of warnings because the tool seems to consider that >>> > extracting an attribute (with getAttrib(x, ...)) or extracting the >>> > slot of an S4 object (with GET_SLOT(x, ...) or R_do_slot(x, ...)) >>> > returns an SEXP that needs protection. I always assumed that it >>> > didn't because my understanding is that the returned SEXP is pointing >>> > to a part of a pre-existing object ('x') and not to a newly created >>> > one. So I decided I could treat it like the SEXP returned by >>> > VECTOR_ELT(), which, AFAIK, doesn't need protection. >>> > > So I suspect these warnings are false positives but I'm not 100% >>> sure. >>> >>> If you are not 100% sure then you should protect :-) >>> >>> There are some cases, in particular related to compact row names on >>> data frames, where getAttrib will allocate. >> >> Seriously? So setAttrib(x, ..., getAttrib) is not going to be a no-op >> anymore? Should I worry that VECTOR_ELT() will also expand some sort >> of compact list element? Why not keep these things low-level >> getters/setters that return whatever the real thing is and use >> higher-level accessors for returning the expanded version of the thing? > > Seriously: it'sbeen that way since r37807 in 2006. > > If you want to read about some related future directions you can look at > https://svn.r-project.org/R/branches/ALTREP/ALTREP.html. > > luke I was curious about this so I checked out what R-exts had to say involving set/getAttrib. Funnily enough, the example it gives in Section 5.9.4 seems to be incorrect in its UNPROTECTing. #include #include SEXP out(SEXP x, SEXP y) { int nx = length(x), ny = length(y); SEXP ans = PROTECT(allocMatrix(REALSXP, nx, ny)); double *rx = REAL(x), *ry = REAL(y), *rans = REAL(ans); for(int i = 0; i < nx; i++) { double tmp = rx[i]; for(int j = 0; j < ny; j++) rans[i + nx*j] = tmp * ry[j]; } SEXP dimnames = PROTECT(allocVector(VECSXP, 2)); SET_VECTOR_ELT(dimnames, 0, getAttrib(x, R_NamesSymbol)); SET_VECTOR_ELT(dimnames, 1, getAttrib(y, R_NamesSymbol)); setAttrib(ans, R_DimNamesSymbol, dimnames); UNPROTECT(3); return ans; } There are two PROTECT calls but an UNPROTECT(3), which triggers a stack imbalance warning upon trying to run .Call("out", ...) in R. Anyway, getting back to the topic of this thread; if we were to pretend that getAttrib() allocates in the above example, would that mean that both getAttrib() calls now need to be PROTECTed by the developer? Or is this handled somewhere internally? >> >> Thanks, >> H. >> >>> >>> Best, >>> >>> luke >>> >>> > > > > > > > > > > > > > I also get a warning on almost every C++ >>> function I've written, >>> > > > > because >>> > > > > I use the following code to handle exceptions: >>> > > > > > > > > SEXP output=PROTECT(allocVector(...)); >>> > > > > try { >>> > > > > // do something that might raise an exception >>> > > > > } catch (std::exception& e) { >>> > > > > UNPROTECT(1); >>> > > > > throw; // break out of this part of the function >>> > > > > } >>> > > > > UNPROTECT(1); >>> > > > > return output; >>> > > > > > > > > Presumably the check doesn't account for transfer of >>> control to > > > > the >>> > > > > catch block. I find that R itself is pretty good at >>> complaining > > > > about >>> > > > > stack imbalances during execution of tests, examples, etc. >>> > > > > > > > > > 'My' packages >>> > > > > > (Rsamtools, DirichletMultinomial) had several false >>> positives > > > > > (all >>> > > > > > associated with use of an attribute of a protected SEXP), >>> one > > > > > subtle >>> > > > > > problem (a symbol from a PROTECT'ed package name space; >>> the > > > > > symbol >>> > > > > > could >>> > > > > > in theory be an active binding and the value obtained not >>> > > > > > PROTECTed by >>> > > > > > the name space), and a genuine bug >>> > > > > > > > > > > tag = NEW_CHARACTER(n); >>> > > > > > for (int j = 0; j < n; ++j) >>> > > > > > SET_STRING_ELT(tag, j, NA_STRING); >>> > > > > > if ('A' == aux[0]) { >>> > > > > > buf_A = R_alloc(2, sizeof(char)); # >>> <<- bug >>> > > > > > buf_A[1] = '\0'; >>> > > > > > } >>> > > > > > ... >>> > > > > > SET_VECTOR_ELT(tags, i, tag); # PROTECT >>>
Re: [Bioc-devel] PROTECT errors in Bioconductor packages
On 04/08/2017 08:16 AM, Aaron Lun wrote: On 07/04/17 20:46, luke-tier...@uiowa.edu wrote: On Fri, 7 Apr 2017, Hervé Pagès wrote: On 04/07/2017 05:37 AM, luke-tier...@uiowa.edu wrote: On Fri, 7 Apr 2017, Hervé Pagès wrote: On 04/06/2017 03:29 AM, Michael Lawrence wrote: On Thu, Apr 6, 2017 at 2:59 AM, Martin Morgan wrote: On 04/06/2017 05:33 AM, Aaron Lun wrote: The tool is not perfect, so assess each report carefully. I get a lot of warnings because the tool seems to consider that extracting an attribute (with getAttrib(x, ...)) or extracting the slot of an S4 object (with GET_SLOT(x, ...) or R_do_slot(x, ...)) returns an SEXP that needs protection. I always assumed that it didn't because my understanding is that the returned SEXP is pointing to a part of a pre-existing object ('x') and not to a newly created one. So I decided I could treat it like the SEXP returned by VECTOR_ELT(), which, AFAIK, doesn't need protection. So I suspect these warnings are false positives but I'm not 100% sure. If you are not 100% sure then you should protect :-) There are some cases, in particular related to compact row names on data frames, where getAttrib will allocate. Seriously? So setAttrib(x, ..., getAttrib) is not going to be a no-op anymore? Should I worry that VECTOR_ELT() will also expand some sort of compact list element? Why not keep these things low-level getters/setters that return whatever the real thing is and use higher-level accessors for returning the expanded version of the thing? Seriously: it'sbeen that way since r37807 in 2006. If you want to read about some related future directions you can look at https://svn.r-project.org/R/branches/ALTREP/ALTREP.html. luke I was curious about this so I checked out what R-exts had to say involving set/getAttrib. Funnily enough, the example it gives in Section 5.9.4 seems to be incorrect in its UNPROTECTing. #include #include SEXP out(SEXP x, SEXP y) { int nx = length(x), ny = length(y); SEXP ans = PROTECT(allocMatrix(REALSXP, nx, ny)); double *rx = REAL(x), *ry = REAL(y), *rans = REAL(ans); for(int i = 0; i < nx; i++) { double tmp = rx[i]; for(int j = 0; j < ny; j++) rans[i + nx*j] = tmp * ry[j]; } SEXP dimnames = PROTECT(allocVector(VECSXP, 2)); SET_VECTOR_ELT(dimnames, 0, getAttrib(x, R_NamesSymbol)); SET_VECTOR_ELT(dimnames, 1, getAttrib(y, R_NamesSymbol)); setAttrib(ans, R_DimNamesSymbol, dimnames); UNPROTECT(3); return ans; } There are two PROTECT calls but an UNPROTECT(3), which triggers a stack imbalance warning upon trying to run .Call("out", ...) in R. Yes, that should be UNPROTECT(2). svn blame says the error was introduced when allocMatrix() was introduced; prior to that the code had allocVector(), then set dim and dimnames. As for whether to PROTECT or not, my analysis would be... SET_VECTOR_ELT does not (currently) allocate (except on error) so there is no opportunity for the garbage collector to run, hence no need to PROTECT. Further, getAttrib() (currently) allocates only if (1) the attribute is R_RowNamesSymbol and the row names are stored in compact format c(NA_integer_, nrow); or (2) the first argument is a classic pairlist or language SEXP. None of these conditions apply, so the return value of getAttrib() is PROTECTed anyway. Luke's analysis would be more straight-forward: if in doubt, PROTECT. I think Herve, Gabe, and perhaps Michael would take Luke's advice, and maybe also note that my advice, in addition to being an analysis of some surprisingly complicated code by a practitioner of dubious credibility, involves the current state of affairs, and you never know (and apparently ALTREP makes it less certain) what the future will hold. So they'd probably say PROTECT. One might be tempted to write SET_VECTOR_ELT(dimnames, 0, PROTECT(getAttrib(x, R_NamesSymbol))); but I'm not sure whether C guarantees that function arguments are fully evaluated, maybe it's legal for a compiler to evaluate getAttrib(), then do some more work with other arguments, then evaluate PROTECT(), so long as the overall logic is not disrupted. So the 'if in doubt' argument would make me write SEXP nms = PROTECT(getAttrib(x, R_NamesSymbol)); SET_VECTOR_ELT(dimnames, 0, nms); I think , in C is called a 'sequence point'. Google takes me to https://msdn.microsoft.com/en-us/library/azk8zbxd.aspx where it seems like the left operand of ',' are fully evaluated before proceeding, and furthermore that arguments to functions are evaluated before entering the function, implying that it is safe to use the one-liner SET_VECTOR_ELT(dimnames, 0, PROTECT(getAttrib(x, R_NamesSymbol))); At any rate I changed the example in R-exts to UNPROTECT(2), leaving the nuances for further discussion. Martin Anyway, getting back to the topic of this thread; if we were to pretend that getAttrib() allo
Re: [Bioc-devel] PROTECT errors in Bioconductor packages
Martin Morgan wrote: > On 04/08/2017 08:16 AM, Aaron Lun wrote: >> On 07/04/17 20:46, luke-tier...@uiowa.edu wrote: >>> On Fri, 7 Apr 2017, Hervé Pagès wrote: >>> On 04/07/2017 05:37 AM, luke-tier...@uiowa.edu wrote: > On Fri, 7 Apr 2017, Hervé Pagès wrote: > >> On 04/06/2017 03:29 AM, Michael Lawrence wrote: >>> On Thu, Apr 6, 2017 at 2:59 AM, Martin Morgan >>> wrote: On 04/06/2017 05:33 AM, Aaron Lun wrote: >>> The tool is not perfect, so assess each report > carefully. >>> I get a lot of warnings because the tool seems to consider that >> extracting an attribute (with getAttrib(x, ...)) or extracting the >> slot of an S4 object (with GET_SLOT(x, ...) or R_do_slot(x, ...)) >> returns an SEXP that needs protection. I always assumed that it >> didn't because my understanding is that the returned SEXP is >> pointing >> to a part of a pre-existing object ('x') and not to a newly created >> one. So I decided I could treat it like the SEXP returned by >> VECTOR_ELT(), which, AFAIK, doesn't need protection. >>> So I suspect these warnings are false positives but I'm not 100% > sure. > > If you are not 100% sure then you should protect :-) > > There are some cases, in particular related to compact row names on > data frames, where getAttrib will allocate. Seriously? So setAttrib(x, ..., getAttrib) is not going to be a no-op anymore? Should I worry that VECTOR_ELT() will also expand some sort of compact list element? Why not keep these things low-level getters/setters that return whatever the real thing is and use higher-level accessors for returning the expanded version of the thing? >>> >>> Seriously: it'sbeen that way since r37807 in 2006. >>> >>> If you want to read about some related future directions you can >>> look at >>> https://svn.r-project.org/R/branches/ALTREP/ALTREP.html. >>> >>> luke >> >> I was curious about this so I checked out what R-exts had to say >> involving set/getAttrib. Funnily enough, the example it gives in Section >> 5.9.4 seems to be incorrect in its UNPROTECTing. >> >> #include >> #include >> >> SEXP out(SEXP x, SEXP y) >> { >> int nx = length(x), ny = length(y); >> SEXP ans = PROTECT(allocMatrix(REALSXP, nx, ny)); >> double *rx = REAL(x), *ry = REAL(y), *rans = REAL(ans); >> >> for(int i = 0; i < nx; i++) { >> double tmp = rx[i]; >> for(int j = 0; j < ny; j++) >> rans[i + nx*j] = tmp * ry[j]; >> } >> >> SEXP dimnames = PROTECT(allocVector(VECSXP, 2)); >> SET_VECTOR_ELT(dimnames, 0, getAttrib(x, R_NamesSymbol)); >> SET_VECTOR_ELT(dimnames, 1, getAttrib(y, R_NamesSymbol)); >> setAttrib(ans, R_DimNamesSymbol, dimnames); >> >> >> UNPROTECT(3); >> return ans; >> } >> >> There are two PROTECT calls but an UNPROTECT(3), which triggers a stack >> imbalance warning upon trying to run .Call("out", ...) in R. > > Yes, that should be UNPROTECT(2). svn blame says the error was > introduced when allocMatrix() was introduced; prior to that the code > had allocVector(), then set dim and dimnames. > > As for whether to PROTECT or not, my analysis would be... > > SET_VECTOR_ELT does not (currently) allocate (except on error) so > there is no opportunity for the garbage collector to run, hence no > need to PROTECT. > > Further, getAttrib() (currently) allocates only if (1) the attribute > is R_RowNamesSymbol and the row names are stored in compact format > c(NA_integer_, nrow); or (2) the first argument is a classic pairlist > or language SEXP. None of these conditions apply, so the return value > of getAttrib() is PROTECTed anyway. > > Luke's analysis would be more straight-forward: if in doubt, PROTECT. > > I think Herve, Gabe, and perhaps Michael would take Luke's advice, and > maybe also note that my advice, in addition to being an analysis of > some surprisingly complicated code by a practitioner of dubious > credibility, involves the current state of affairs, and you never know > (and apparently ALTREP makes it less certain) what the future will > hold. So they'd probably say PROTECT. > > One might be tempted to write > > SET_VECTOR_ELT(dimnames, 0, PROTECT(getAttrib(x, R_NamesSymbol))); > > but I'm not sure whether C guarantees that function arguments are > fully evaluated, maybe it's legal for a compiler to evaluate > getAttrib(), then do some more work with other arguments, then > evaluate PROTECT(), so long as the overall logic is not disrupted. So > the 'if in doubt' argument would make me write > > SEXP nms = PROTECT(getAttrib(x, R_NamesSymbol)); > SET_VECTOR_ELT(dimnames, 0, nms); > > I think , in C is called a 'sequence point'. Google takes me to > > https://msdn.microsoft.com/en-us/library/azk8zbxd.aspx > > where it seems like the left operand of ',' are fully evaluated before > proceeding, and furthermore that argu
Re: [Bioc-devel] PROTECT errors in Bioconductor packages
On 04/08/2017 06:50 AM, Martin Morgan wrote: On 04/08/2017 08:16 AM, Aaron Lun wrote: On 07/04/17 20:46, luke-tier...@uiowa.edu wrote: On Fri, 7 Apr 2017, Hervé Pagès wrote: On 04/07/2017 05:37 AM, luke-tier...@uiowa.edu wrote: On Fri, 7 Apr 2017, Hervé Pagès wrote: On 04/06/2017 03:29 AM, Michael Lawrence wrote: On Thu, Apr 6, 2017 at 2:59 AM, Martin Morgan wrote: On 04/06/2017 05:33 AM, Aaron Lun wrote: The tool is not perfect, so assess each report carefully. I get a lot of warnings because the tool seems to consider that extracting an attribute (with getAttrib(x, ...)) or extracting the slot of an S4 object (with GET_SLOT(x, ...) or R_do_slot(x, ...)) returns an SEXP that needs protection. I always assumed that it didn't because my understanding is that the returned SEXP is pointing to a part of a pre-existing object ('x') and not to a newly created one. So I decided I could treat it like the SEXP returned by VECTOR_ELT(), which, AFAIK, doesn't need protection. So I suspect these warnings are false positives but I'm not 100% sure. If you are not 100% sure then you should protect :-) There are some cases, in particular related to compact row names on data frames, where getAttrib will allocate. Seriously? So setAttrib(x, ..., getAttrib) is not going to be a no-op anymore? Should I worry that VECTOR_ELT() will also expand some sort of compact list element? Why not keep these things low-level getters/setters that return whatever the real thing is and use higher-level accessors for returning the expanded version of the thing? Seriously: it'sbeen that way since r37807 in 2006. If you want to read about some related future directions you can look at https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.r-2Dproject.org_R_branches_ALTREP_ALTREP.html&d=DwIF-g&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ECmvCrpSP99jd6o3J4LkX4nL1PKJiNM1Ky6_-c7ob5k&s=S-eq87dmcXe7_GR61c5ZPGzqT9V2booIH5P7G_Jch18&e= . luke I was curious about this so I checked out what R-exts had to say involving set/getAttrib. Funnily enough, the example it gives in Section 5.9.4 seems to be incorrect in its UNPROTECTing. #include #include SEXP out(SEXP x, SEXP y) { int nx = length(x), ny = length(y); SEXP ans = PROTECT(allocMatrix(REALSXP, nx, ny)); double *rx = REAL(x), *ry = REAL(y), *rans = REAL(ans); for(int i = 0; i < nx; i++) { double tmp = rx[i]; for(int j = 0; j < ny; j++) rans[i + nx*j] = tmp * ry[j]; } SEXP dimnames = PROTECT(allocVector(VECSXP, 2)); SET_VECTOR_ELT(dimnames, 0, getAttrib(x, R_NamesSymbol)); SET_VECTOR_ELT(dimnames, 1, getAttrib(y, R_NamesSymbol)); setAttrib(ans, R_DimNamesSymbol, dimnames); UNPROTECT(3); return ans; } There are two PROTECT calls but an UNPROTECT(3), which triggers a stack imbalance warning upon trying to run .Call("out", ...) in R. Yes, that should be UNPROTECT(2). svn blame says the error was introduced when allocMatrix() was introduced; prior to that the code had allocVector(), then set dim and dimnames. As for whether to PROTECT or not, my analysis would be... SET_VECTOR_ELT does not (currently) allocate (except on error) so there is no opportunity for the garbage collector to run, hence no need to PROTECT. Further, getAttrib() (currently) allocates only if (1) the attribute is R_RowNamesSymbol and the row names are stored in compact format c(NA_integer_, nrow); or (2) the first argument is a classic pairlist or language SEXP. None of these conditions apply, so the return value of getAttrib() is PROTECTed anyway. Luke's analysis would be more straight-forward: if in doubt, PROTECT. I think Herve, Gabe, and perhaps Michael would take Luke's advice, and maybe also note that my advice, in addition to being an analysis of some surprisingly complicated code by a practitioner of dubious credibility, involves the current state of affairs, and you never know (and apparently ALTREP makes it less certain) what the future will hold. So they'd probably say PROTECT. One might be tempted to write SET_VECTOR_ELT(dimnames, 0, PROTECT(getAttrib(x, R_NamesSymbol))); but I'm not sure whether C guarantees that function arguments are fully evaluated, maybe it's legal for a compiler to evaluate getAttrib(), then do some more work with other arguments, then evaluate PROTECT(), so long as the overall logic is not disrupted. So the 'if in doubt' argument would make me write SEXP nms = PROTECT(getAttrib(x, R_NamesSymbol)); SET_VECTOR_ELT(dimnames, 0, nms); I think , in C is called a 'sequence point'. Google takes me to https://urldefense.proofpoint.com/v2/url?u=https-3A__msdn.microsoft.com_en-2Dus_library_azk8zbxd.aspx&d=DwIF-g&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ECmvCrpSP99jd6o3J4LkX4nL1PKJiNM1Ky6_-c7ob5k&s=ekY5D7Za0NSpYmZxnR3ONu7u8f_qyDme47VeHsBWp6w&e= where it seems like the left operan
Re: [Bioc-devel] PROTECT errors in Bioconductor packages
On 04/08/2017 12:29 PM, Aaron Lun wrote: Martin Morgan wrote: On 04/08/2017 08:16 AM, Aaron Lun wrote: On 07/04/17 20:46, luke-tier...@uiowa.edu wrote: On Fri, 7 Apr 2017, Hervé Pagès wrote: On 04/07/2017 05:37 AM, luke-tier...@uiowa.edu wrote: On Fri, 7 Apr 2017, Hervé Pagès wrote: On 04/06/2017 03:29 AM, Michael Lawrence wrote: On Thu, Apr 6, 2017 at 2:59 AM, Martin Morgan wrote: On 04/06/2017 05:33 AM, Aaron Lun wrote: The tool is not perfect, so assess each report carefully. I get a lot of warnings because the tool seems to consider that extracting an attribute (with getAttrib(x, ...)) or extracting the slot of an S4 object (with GET_SLOT(x, ...) or R_do_slot(x, ...)) returns an SEXP that needs protection. I always assumed that it didn't because my understanding is that the returned SEXP is pointing to a part of a pre-existing object ('x') and not to a newly created one. So I decided I could treat it like the SEXP returned by VECTOR_ELT(), which, AFAIK, doesn't need protection. So I suspect these warnings are false positives but I'm not 100% sure. If you are not 100% sure then you should protect :-) There are some cases, in particular related to compact row names on data frames, where getAttrib will allocate. Seriously? So setAttrib(x, ..., getAttrib) is not going to be a no-op anymore? Should I worry that VECTOR_ELT() will also expand some sort of compact list element? Why not keep these things low-level getters/setters that return whatever the real thing is and use higher-level accessors for returning the expanded version of the thing? Seriously: it'sbeen that way since r37807 in 2006. If you want to read about some related future directions you can look at https://svn.r-project.org/R/branches/ALTREP/ALTREP.html. luke I was curious about this so I checked out what R-exts had to say involving set/getAttrib. Funnily enough, the example it gives in Section 5.9.4 seems to be incorrect in its UNPROTECTing. #include #include SEXP out(SEXP x, SEXP y) { int nx = length(x), ny = length(y); SEXP ans = PROTECT(allocMatrix(REALSXP, nx, ny)); double *rx = REAL(x), *ry = REAL(y), *rans = REAL(ans); for(int i = 0; i < nx; i++) { double tmp = rx[i]; for(int j = 0; j < ny; j++) rans[i + nx*j] = tmp * ry[j]; } SEXP dimnames = PROTECT(allocVector(VECSXP, 2)); SET_VECTOR_ELT(dimnames, 0, getAttrib(x, R_NamesSymbol)); SET_VECTOR_ELT(dimnames, 1, getAttrib(y, R_NamesSymbol)); setAttrib(ans, R_DimNamesSymbol, dimnames); UNPROTECT(3); return ans; } There are two PROTECT calls but an UNPROTECT(3), which triggers a stack imbalance warning upon trying to run .Call("out", ...) in R. Yes, that should be UNPROTECT(2). svn blame says the error was introduced when allocMatrix() was introduced; prior to that the code had allocVector(), then set dim and dimnames. As for whether to PROTECT or not, my analysis would be... SET_VECTOR_ELT does not (currently) allocate (except on error) so there is no opportunity for the garbage collector to run, hence no need to PROTECT. Further, getAttrib() (currently) allocates only if (1) the attribute is R_RowNamesSymbol and the row names are stored in compact format c(NA_integer_, nrow); or (2) the first argument is a classic pairlist or language SEXP. None of these conditions apply, so the return value of getAttrib() is PROTECTed anyway. Luke's analysis would be more straight-forward: if in doubt, PROTECT. I think Herve, Gabe, and perhaps Michael would take Luke's advice, and maybe also note that my advice, in addition to being an analysis of some surprisingly complicated code by a practitioner of dubious credibility, involves the current state of affairs, and you never know (and apparently ALTREP makes it less certain) what the future will hold. So they'd probably say PROTECT. One might be tempted to write SET_VECTOR_ELT(dimnames, 0, PROTECT(getAttrib(x, R_NamesSymbol))); but I'm not sure whether C guarantees that function arguments are fully evaluated, maybe it's legal for a compiler to evaluate getAttrib(), then do some more work with other arguments, then evaluate PROTECT(), so long as the overall logic is not disrupted. So the 'if in doubt' argument would make me write SEXP nms = PROTECT(getAttrib(x, R_NamesSymbol)); SET_VECTOR_ELT(dimnames, 0, nms); I think , in C is called a 'sequence point'. Google takes me to https://msdn.microsoft.com/en-us/library/azk8zbxd.aspx where it seems like the left operand of ',' are fully evaluated before proceeding, and furthermore that arguments to functions are evaluated before entering the function, implying that it is safe to use the one-liner SET_VECTOR_ELT(dimnames, 0, PROTECT(getAttrib(x, R_NamesSymbol))); At any rate I changed the example in R-exts to UNPROTECT(2), leaving the nuances for further discussion. Martin I wonder if the following is a sensible idea: int Rf_num
Re: [Bioc-devel] PROTECT errors in Bioconductor packages
Martin Morgan wrote: > On 04/08/2017 12:29 PM, Aaron Lun wrote: >> Martin Morgan wrote: >>> On 04/08/2017 08:16 AM, Aaron Lun wrote: On 07/04/17 20:46, luke-tier...@uiowa.edu wrote: > On Fri, 7 Apr 2017, Hervé Pagès wrote: > >> On 04/07/2017 05:37 AM, luke-tier...@uiowa.edu wrote: >>> On Fri, 7 Apr 2017, Hervé Pagès wrote: >>> On 04/06/2017 03:29 AM, Michael Lawrence wrote: > On Thu, Apr 6, 2017 at 2:59 AM, Martin Morgan > wrote: >> On 04/06/2017 05:33 AM, Aaron Lun wrote: > The tool is not perfect, so assess each report >>> carefully. > I get a lot of warnings because the tool seems to consider that extracting an attribute (with getAttrib(x, ...)) or extracting the slot of an S4 object (with GET_SLOT(x, ...) or R_do_slot(x, ...)) returns an SEXP that needs protection. I always assumed that it didn't because my understanding is that the returned SEXP is pointing to a part of a pre-existing object ('x') and not to a newly created one. So I decided I could treat it like the SEXP returned by VECTOR_ELT(), which, AFAIK, doesn't need protection. > So I suspect these warnings are false positives but I'm not 100% >>> sure. >>> >>> If you are not 100% sure then you should protect :-) >>> >>> There are some cases, in particular related to compact row >>> names on >>> data frames, where getAttrib will allocate. >> >> Seriously? So setAttrib(x, ..., getAttrib) is not going to be a >> no-op >> anymore? Should I worry that VECTOR_ELT() will also expand some sort >> of compact list element? Why not keep these things low-level >> getters/setters that return whatever the real thing is and use >> higher-level accessors for returning the expanded version of the >> thing? > > Seriously: it'sbeen that way since r37807 in 2006. > > If you want to read about some related future directions you can > look at > https://svn.r-project.org/R/branches/ALTREP/ALTREP.html. > > luke I was curious about this so I checked out what R-exts had to say involving set/getAttrib. Funnily enough, the example it gives in Section 5.9.4 seems to be incorrect in its UNPROTECTing. #include #include SEXP out(SEXP x, SEXP y) { int nx = length(x), ny = length(y); SEXP ans = PROTECT(allocMatrix(REALSXP, nx, ny)); double *rx = REAL(x), *ry = REAL(y), *rans = REAL(ans); for(int i = 0; i < nx; i++) { double tmp = rx[i]; for(int j = 0; j < ny; j++) rans[i + nx*j] = tmp * ry[j]; } SEXP dimnames = PROTECT(allocVector(VECSXP, 2)); SET_VECTOR_ELT(dimnames, 0, getAttrib(x, R_NamesSymbol)); SET_VECTOR_ELT(dimnames, 1, getAttrib(y, R_NamesSymbol)); setAttrib(ans, R_DimNamesSymbol, dimnames); UNPROTECT(3); return ans; } There are two PROTECT calls but an UNPROTECT(3), which triggers a stack imbalance warning upon trying to run .Call("out", ...) in R. >>> >>> Yes, that should be UNPROTECT(2). svn blame says the error was >>> introduced when allocMatrix() was introduced; prior to that the code >>> had allocVector(), then set dim and dimnames. >>> >>> As for whether to PROTECT or not, my analysis would be... >>> >>> SET_VECTOR_ELT does not (currently) allocate (except on error) so >>> there is no opportunity for the garbage collector to run, hence no >>> need to PROTECT. >>> >>> Further, getAttrib() (currently) allocates only if (1) the attribute >>> is R_RowNamesSymbol and the row names are stored in compact format >>> c(NA_integer_, nrow); or (2) the first argument is a classic pairlist >>> or language SEXP. None of these conditions apply, so the return value >>> of getAttrib() is PROTECTed anyway. >>> >>> Luke's analysis would be more straight-forward: if in doubt, PROTECT. >>> >>> I think Herve, Gabe, and perhaps Michael would take Luke's advice, and >>> maybe also note that my advice, in addition to being an analysis of >>> some surprisingly complicated code by a practitioner of dubious >>> credibility, involves the current state of affairs, and you never know >>> (and apparently ALTREP makes it less certain) what the future will >>> hold. So they'd probably say PROTECT. >>> >>> One might be tempted to write >>> >>> SET_VECTOR_ELT(dimnames, 0, PROTECT(getAttrib(x, R_NamesSymbol))); >>> >>> but I'm not sure whether C guarantees that function arguments are >>> fully evaluated, maybe it's legal for a compiler to evaluate >>> getAttrib(), then do some more work with other arguments, then >>> evaluate PROTECT(), so long as the overall logic is not disrupted. So >>> the 'if in doubt' argument would make me write >>> >>>