Over the past few months, I have been working on testing the Rcpp packages using RcppDeepState in the cluster. When we fuzz test each Rcpp function-specific testharness I have found issues in 134 packages.
The List of packages that we found issues can be found here. This web page lists the packages with Issues in exported functions and unexported functions.
RcppDeepState detected 11 packages with issues in exported functions and 128 packages with issues in unexported functions.
Clicking on a package redirects you to a web page with a table. The Table consists of 5 columns:
- name: This gives the name of the function and its relation with the package (
:::represents an unexported function,::represents exported function). - inputs: gives the arguments passed onto the function to generate the Valgrind errors. These files are usually .qs files and to read the files we need to use qread.
- message: The message Valgrind generated.
- file.line: shows the name of the file and line number where the issue occurred.
- valgrind_log: This file gives the complete Valgrind log trace.
- executable.file: To reproduce the same error on your system, copy the file to your system, and execute it under Valgrind.
Reproducing the Results
I am reproducing the results of the AGread package and get_VM_C function.
- First create an R file:
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akhila@ml-experiments:~$ nano AGread:::get_VM_C-test.R
- Save the executable file contents in AGread:::get_VM_C-test.R:
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testlist <- list(x = c(-9.55582196017401e+29, -4.90459010763407e-29, 4.90985848662137e-132, 1.34087923799627e-99, -2.83758126022851e-214, -3.86582708286114e+118, 1.56442933387274e-40, 7.80171305823656e-14, -1.83590112917186e-143, -2.12225393135038e-27, -2.39035558481144e+94, 1.39381080421907e+78, 8.09020071287152e+217, 3.20154172554715e+166, -1.07544081057137e+142, -1.22716245834473e+249, 0.0045576245392274, 4.110270279077e-119, -2.13090432437324e-232, -2.00173720606795e-54, 29540115.857733, 1.14560222054498e+104, -1.51179353689993e+219, 1.85583157125209e-183, 5.34002291753896e+279, 3.163119668952e+220, -2.84339292934663e+164, 5.13557333556931e-82, -4.11812482604814e-235, 9.56040251934328e-42, -2.59207149164433e-228, 1.2158458081832e-222, -1.74238018159446e+182, 7.41245245658227e-295, -4.00558303551056e+236, 3.47151817076085e-119, 4.10403783345669e-88, -7.40647194992956e+299, -2.19378089629216e+123, -1.54830595119915e-41, -2.54764432636554e+33, 2.48050399286568e+82, 3.22488547429564e-46, -7.02949111491804e+254, -7.61353710150679e+209, -17873921569877248000, -4.78466694563666e+177, 9.36219676678338e-189, 4.39158645590191e+53, -2.88703981054995e-216, 2.78090680147068e-174, 1.48246692773206e-213, -4.99040512819108e-30, 2.24505481320356e+72, -Inf, -3.81316040338393e+279, -2.59826575494024e+116, 9.66176246763658e+303, -8.7275455542068e-49, 2.49022343960829e+238, 9.23934088471241e+265, -9.44640342943815e+145, -7.78813268347435e-290, -6.86657422733089e+196, 1.2158458081832e-222, 4.38927944252164e-14, 1.2158458081832e-222, -2.79793587635494e-150, 1.21474661935272e-71, 5.11142779337243e-26, 3.61605547103826e+106, -1.29008433506166e+98, -4.71290430009938e+192, 2.16276193556995e-78, Inf, -73702024288693120, 3.67680763978728e+303, 6.79444019345624e+289, 1.57080783318714e-223, 2.44989196103371e-214, 2.14683789541018e+191, -1.56271793377671e+242, -8.12565116309796e-10, -2.15359476910305e-49, 6.45169663269538e+246, -8.81729169866251e-223, -1.72994822845411e-121, -1.62164229453157e+62, -7.11519061213384e-291, -5.96039842159441e+297, 1.78946373645738e-58, -2477302959913879552, 5.3208487330171e+104, 0), y = c(-3.26554114015345e+152, 3.18206849979581e-100, -1.56175745908205e-27, -1.53699520139895e-168, -3.45365770774053e-208, 1.64987860536309e+306, -8.4875906377816e+297, -2.24827554179635e+194, 3.33229472935506e-79, -1.74384352802101e+258, -1.48447741823703e+292, 1.13714330989583e-117, NaN, 2.26233751114504e-222, -1.01722477369572e+190, -Inf, 3.76448348749029e+191, NaN, -8.35948760513993e+225, -1.70730166016845e-156, 1.27082426005613e+293, -4.58747899892024e-154, 2.0190979016347e+305, -9.03381870805068e+126, 9.95505452219636e+88, -8.94698245383292e+169, 9.07030335339282e-230, -2.60502401687064e+201, 1.64945789439185e-87, 4.99710237875113e-12, -7.17761868684456e-304, -4.3658043201413e+77, -1.03383180363943e+79, -1.06914531395343e+103, -5.30285459292229e+216, -3.0565209504357e-130, -1.71729511302952e-159, -2.17924555299383e-269, 4.28642965121133e-95, -2.15390099076119e-268, -1.72195489251578e-249, 6.58367713694062e+280, 2.46336940755175e+76, -5.20477740765405e-262, 1.39905108202245e-99, 9.88192228952185e-25, -3.61551136030365e-45, -1.74619475327206e-101, 3.6666299164515e-120, -Inf, 7.17066122458692e-250, -2.378202461375e-231, -2.91706999191851e-31, 2.91754200415233e-52, -8.15309037183729e+138, -2.56543721632249e-216, 6.42400059829704e-260, -1.16133602395052e+62, 2.67059509197991e+205, 4.65822589964347e-299, 9.1666663674939e+232, 1.65110215729462e+101, Inf, 1.15230597511972e+138, 1.97267429248055e+163, 3.97553287750579e-113, -6.57481557461354e-05, 1.35715728528751e+180, -2.96150696524813e+235, -4.24956568308809e+21, 2.41521697023484e-123, -1.22597501534853e-99, 1.19023625716e+88, -1.19015768274565e-116, 1.29054759607899e+35, 2.64241368191397e-72, 4.58920593280658e+173, 1.62627920428666e-289, -1.47803007853383e+144, -6.15463639791464e-89, -1.05364750681707e+169, -2.45565549861933e-224, -1.98728021213713e-262, -2.92127556842489e-21, 6918497.86511318, 25063312106601372, -7.19944401535096e-57, -1.91849726575268e-287, 7.21116286537801e-227, -3.60207037565642e+110, -7.26637752801978e+235, 1.07246462937891e+118, 0), z = c(-4.84932478603115e+123, NaN, Inf, -5.7275290747398e+192, 5.58421313925681e+204, -2.28660386920664e+173, -1.97697637114179e-69, 3.38075822495626e+149, 4.32081599986107e-209, -1.29313617432814e-14, 4.71547010058052e-43, -250.127205510875, 1.46149092470503e+123, 9.40731273350158e-07, -2.12675472790339e-194, -1.65103679993611e-37, -1.86379765044409e-281, NaN, 6.08867901867669e+206, 5.98780222943024e-177, 5.3714752216163e+289, -3.45950447436657e+183, 1.49124941875444e+123, 1.5271822412807e+69, -1.11744397039332e+248, 2.54518372279385e+39, -1.89122208320009e+202, 1.32649719153595e-258, -4.98888109635576e-11, 2.78713015973591e-92, -2.19763919263402e-262, 1.0259819645017e-63, -6.65300857906418e+44, -7.06992781198399e-163, 1.97837196945601e+50, 8.66847551530699e+52, NA, 5.05828908606344e+82, -6.61537374830274e+258, -5.53117588312793e-242, -7.44546802785227e+176, 5.89018085455203e+172, 3.11179473946186e-269, 4.27273222011121e-258, 1.81205902881488e+292, 3.63659296687523e+150, -1.76238047328413e-172, 3.21076982012694e+97, -1.97697562608513e-32, -7.48931142066971e+103, -1.6935534783091e-223, -2.23568438386655e-290, 4.60738393919573e-112, -1.67433275761641, -1.45002600215092e-210, 4.589781857875e+224, -7.72209849174466e-23, 5.90208266243812e+79, -3.83061650675902e-208, 1.86512759599204e+231, 6.41943730702922e+301, 9.46104617841303e-28, 1.29593850784906e+277, -3.01659138117281e-306, -3.10960825603861e-93, -1.66248253051722e+24, 2.57961067707722e-78, 4.73689044138891e-82, -4.0456986884011e+22, -0.019009825744731, -1.52390505473001e-231, -1.14984339579174e+177, 1.66207346607985e+119, -1.56225281476421e-174, -3.19832453218957e-155, -Inf))
result <- do.call(AGread:::get_VM_C,testlist)
str(result)
- Now execute the file under Valgrind :
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akhila@ml-experiments:~$ R -d valgrind --vanilla < AGread:::get_VM_C-test.R
==2137988== Memcheck, a memory error detector
==2137988== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==2137988== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info
==2137988== Command: /usr/lib/R/bin/exec/R --vanilla
==2137988==
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> testlist <- list(x = c(-9.55582196017401e+29, -4.90459010763407e-29, 4.90985848662137e-132, 1.34087923799627e-99, -2.83758126022851e-214, -3.86582708286114e+118, 1.56442933387274e-40, 7.80171305823656e-14, -1.83590112917186e-143, -2.12225393135038e-27, -2.39035558481144e+94, 1.39381080421907e+78, 8.09020071287152e+217, 3.20154172554715e+166, -1.07544081057137e+142, -1.22716245834473e+249, 0.0045576245392274, 4.110270279077e-119, -2.13090432437324e-232, -2.00173720606795e-54, 29540115.857733, 1.14560222054498e+104, -1.51179353689993e+219, 1.85583157125209e-183, 5.34002291753896e+279, 3.163119668952e+220, -2.84339292934663e+164, 5.13557333556931e-82, -4.11812482604814e-235, 9.56040251934328e-42, -2.59207149164433e-228, 1.2158458081832e-222, -1.74238018159446e+182, 7.41245245658227e-295, -4.00558303551056e+236, 3.47151817076085e-119, 4.10403783345669e-88, -7.40647194992956e+299, -2.19378089629216e+123, -1.54830595119915e-41, -2.54764432636554e+33, 2.48050399286568e+82, 3.22488547429564e-46, -7.02949111491804e+254, -7.61353710150679e+209, -17873921569877248000, -4.78466694563666e+177, 9.36219676678338e-189, 4.39158645590191e+53, -2.88703981054995e-216, 2.78090680147068e-174, 1.48246692773206e-213, -4.99040512819108e-30, 2.24505481320356e+72, -Inf, -3.81316040338393e+279, -2.59826575494024e+116, 9.66176246763658e+303, -8.7275455542068e-49, 2.49022343960829e+238, 9.23934088471241e+265, -9.44640342943815e+145, -7.78813268347435e-290, -6.86657422733089e+196, 1.2158458081832e-222, 4.38927944252164e-14, 1.2158458081832e-222, -2.79793587635494e-150, 1.21474661935272e-71, 5.11142779337243e-26, 3.61605547103826e+106, -1.29008433506166e+98, -4.71290430009938e+192, 2.16276193556995e-78, Inf, -73702024288693120, 3.67680763978728e+303, 6.79444019345624e+289, 1.57080783318714e-223, 2.44989196103371e-214, 2.14683789541018e+191, -1.56271793377671e+242, -8.12565116309796e-10, -2.15359476910305e-49, 6.45169663269538e+246, -8.81729169866251e-223, -1.72994822845411e-121, -1.62164229453157e+62, -7.11519061213384e-291, -5.96039842159441e+297, 1.78946373645738e-58, -2477302959913879552, 5.3208487330171e+104, 0), y = c(-3.26554114015345e+152, 3.18206849979581e-100, -1.56175745908205e-27, -1.53699520139895e-168, -3.45365770774053e-208, 1.64987860536309e+306, -8.4875906377816e+297, -2.24827554179635e+194, 3.33229472935506e-79, -1.74384352802101e+258, -1.48447741823703e+292, 1.13714330989583e-117, NaN, 2.26233751114504e-222, -1.01722477369572e+190, -Inf, 3.76448348749029e+191, NaN, -8.35948760513993e+225, -1.70730166016845e-156, 1.27082426005613e+293, -4.58747899892024e-154, 2.0190979016347e+305, -9.03381870805068e+126, 9.95505452219636e+88, -8.94698245383292e+169, 9.07030335339282e-230, -2.60502401687064e+201, 1.64945789439185e-87, 4.99710237875113e-12, -7.17761868684456e-304, -4.3658043201413e+77, -1.03383180363943e+79, -1.06914531395343e+103, -5.30285459292229e+216, -3.0565209504357e-130, -1.71729511302952e-159, -2.17924555299383e-269, 4.28642965121133e-95, -2.15390099076119e-268, -1.72195489251578e-249, 6.58367713694062e+280, 2.46336940755175e+76, -5.20477740765405e-262, 1.39905108202245e-99, 9.88192228952185e-25, -3.61551136030365e-45, -1.74619475327206e-101, 3.6666299164515e-120, -Inf, 7.17066122458692e-250, -2.378202461375e-231, -2.91706999191851e-31, 2.91754200415233e-52, -8.15309037183729e+138, -2.56543721632249e-216, 6.42400059829704e-260, -1.16133602395052e+62, 2.67059509197991e+205, 4.65822589964347e-299, 9.1666663674939e+232, 1.65110215729462e+101, Inf, 1.15230597511972e+138, 1.97267429248055e+163, 3.97553287750579e-113, -6.57481557461354e-05, 1.35715728528751e+180, -2.96150696524813e+235, -4.24956568308809e+21, 2.41521697023484e-123, -1.22597501534853e-99, 1.19023625716e+88, -1.19015768274565e-116, 1.29054759607899e+35, 2.64241368191397e-72, 4.58920593280658e+173, 1.62627920428666e-289, -1.47803007853383e+144, -6.15463639791464e-89, -1.05364750681707e+169, -2.45565549861933e-224, -1.98728021213713e-262, -2.92127556842489e-21, 6918497.86511318, 25063312106601372, -7.19944401535096e+ -57, -1.91849726575268e-287, 7.21116286537801e-227, -3.60207037565642e+110, -7.26637752801978e+235, 1.07246462937891e+118, 0), z = c(-4.84932478603115e+123, NaN, Inf, -5.7275290747398e+192, 5.58421313925681e+204, -2.28660386920664e+173, -1.97697637114179e-69, 3.38075822495626e+149, 4.32081599986107e-209, -1.29313617432814e-14, 4.71547010058052e-43, -250.127205510875, 1.46149092470503e+123, 9.40731273350158e-07, -2.12675472790339e-194, -1.65103679993611e-37, -1.86379765044409e-281, NaN, 6.08867901867669e+206, 5.98780222943024e-177, 5.3714752216163e+289, -3.45950447436657e+183, 1.49124941875444e+123, 1.5271822412807e+69, -1.11744397039332e+248, 2.54518372279385e+39, -1.89122208320009e+202, 1.32649719153595e-258, -4.98888109635576e-11, 2.78713015973591e-92, -2.19763919263402e-262, 1.0259819645017e-63, -6.65300857906418e+44, -7.06992781198399e-163, 1.97837196945601e+50, 8.66847551530699e+52, NA, 5.05828908606344e+82, -6.61537374830274e+258, -5.53117588312793e-242, -7.44546802785227e+176, 5.89018085455203e+172, 3.11179473946186e-269, 4.27273222011121e-258, 1.81205902881488e+292, 3.63659296687523e+150, -1.76238047328413e-172, 3.21076982012694e+97, -1.97697562608513e-32, -7.48931142066971e+103, -1.6935534783091e-223, -2.23568438386655e-290, 4.60738393919573e-112, -1.67433275761641, -1.45002600215092e-210, 4.589781857875e+224, -7.72209849174466e-23, 5.90208266243812e+79, -3.83061650675902e-208, 1.86512759599204e+231, 6.41943730702922e+301, 9.46104617841303e-28, 1.29593850784906e+277, -3.01659138117281e-306, -3.10960825603861e-93, -1.66248253051722e+24, 2.57961067707722e-78, 4.73689044138891e-82, -4.0456986884011e+22, -0.019009825744731, -1.52390505473001e-231, -1.14984339579174e+177, 1.66207346607985e+119, -1.56225281476421e-174, -3.19832453218957e-155, -Inf))
> result <- do.call(AGread:::get_VM_C,testlist)
==2137988== Invalid read of size 8
==2137988== at 0xD16620E: get_VM_C(Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) (get_VM_C.cpp:22)
==2137988== by 0xD15AAB9: _AGread_get_VM_C (RcppExports.cpp:17)
==2137988== by 0x493B475: ??? (in /usr/lib/R/lib/libR.so)
==2137988== by 0x49716CF: ??? (in /usr/lib/R/lib/libR.so)
==2137988== by 0x498D60F: Rf_eval (in /usr/lib/R/lib/libR.so)
==2137988== by 0x498F41E: ??? (in /usr/lib/R/lib/libR.so)
==2137988== by 0x4990252: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
==2137988== by 0x498D729: Rf_eval (in /usr/lib/R/lib/libR.so)
==2137988== by 0x49081CC: ??? (in /usr/lib/R/lib/libR.so)
==2137988== by 0x49716CF: ??? (in /usr/lib/R/lib/libR.so)
==2137988== by 0x498D60F: Rf_eval (in /usr/lib/R/lib/libR.so)
==2137988== by 0x498F41E: ??? (in /usr/lib/R/lib/libR.so)
==2137988== Address 0x9397af0 is 0 bytes after a block of size 656 alloc'd
==2137988== at 0x483B7F3: malloc (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_memcheck-amd64-linux.so)
==2137988== by 0x49CA3E4: Rf_allocVector3 (in /usr/lib/R/lib/libR.so)
==2137988== by 0xD166102: import_sugar_expression<true, Rcpp::sugar::Pow<14, true, Rcpp::Vector<14, Rcpp::PreserveStorage>, int> > (Vector.h:1070)
==2137988== by 0xD166102: Vector<true, Rcpp::sugar::Pow<14, true, Rcpp::Vector<14, Rcpp::PreserveStorage>, int> > (Vector.h:165)
==2137988== by 0xD166102: get_VM_C(Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) (get_VM_C.cpp:19)
==2137988== by 0xD15AAB9: _AGread_get_VM_C (RcppExports.cpp:17)
==2137988== by 0x493B475: ??? (in /usr/lib/R/lib/libR.so)
==2137988== by 0x49716CF: ??? (in /usr/lib/R/lib/libR.so)
==2137988== by 0x498D60F: Rf_eval (in /usr/lib/R/lib/libR.so)
==2137988== by 0x498F41E: ??? (in /usr/lib/R/lib/libR.so)
==2137988== by 0x4990252: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
==2137988== by 0x498D729: Rf_eval (in /usr/lib/R/lib/libR.so)
==2137988== by 0x49081CC: ??? (in /usr/lib/R/lib/libR.so)
==2137988== by 0x49716CF: ??? (in /usr/lib/R/lib/libR.so)
==2137988==
==2137988== Invalid read of size 8
==2137988== at 0xD166203: get_VM_C(Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) (get_VM_C.cpp:22)
==2137988== by 0xD15AAB9: _AGread_get_VM_C (RcppExports.cpp:17)
==2137988== by 0x493B475: ??? (in /usr/lib/R/lib/libR.so)
==2137988== by 0x49716CF: ??? (in /usr/lib/R/lib/libR.so)
==2137988== by 0x498D60F: Rf_eval (in /usr/lib/R/lib/libR.so)
==2137988== by 0x498F41E: ??? (in /usr/lib/R/lib/libR.so)
==2137988== by 0x4990252: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
==2137988== by 0x498D729: Rf_eval (in /usr/lib/R/lib/libR.so)
==2137988== by 0x49081CC: ??? (in /usr/lib/R/lib/libR.so)
==2137988== by 0x49716CF: ??? (in /usr/lib/R/lib/libR.so)
==2137988== by 0x498D60F: Rf_eval (in /usr/lib/R/lib/libR.so)
==2137988== by 0x498F41E: ??? (in /usr/lib/R/lib/libR.so)
==2137988== Address 0x83b7758 is 0 bytes after a block of size 792 alloc'd
==2137988== at 0x483B7F3: malloc (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_memcheck-amd64-linux.so)
==2137988== by 0x49CA3E4: Rf_allocVector3 (in /usr/lib/R/lib/libR.so)
==2137988== by 0xD165FFD: import_sugar_expression<true, Rcpp::sugar::Pow<14, true, Rcpp::Vector<14, Rcpp::PreserveStorage>, int> > (Vector.h:1070)
==2137988== by 0xD165FFD: Vector<true, Rcpp::sugar::Pow<14, true, Rcpp::Vector<14, Rcpp::PreserveStorage>, int> > (Vector.h:165)
==2137988== by 0xD165FFD: get_VM_C(Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) (get_VM_C.cpp:18)
==2137988== by 0xD15AAB9: _AGread_get_VM_C (RcppExports.cpp:17)
==2137988== by 0x493B475: ??? (in /usr/lib/R/lib/libR.so)
==2137988== by 0x49716CF: ??? (in /usr/lib/R/lib/libR.so)
==2137988== by 0x498D60F: Rf_eval (in /usr/lib/R/lib/libR.so)
==2137988== by 0x498F41E: ??? (in /usr/lib/R/lib/libR.so)
==2137988== by 0x4990252: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
==2137988== by 0x498D729: Rf_eval (in /usr/lib/R/lib/libR.so)
==2137988== by 0x49081CC: ??? (in /usr/lib/R/lib/libR.so)
==2137988== by 0x49716CF: ??? (in /usr/lib/R/lib/libR.so)
==2137988==
> str(result)
num [1:94] 3.27e+152 NaN Inf Inf Inf ...
>
==2137988==
==2137988== HEAP SUMMARY:
==2137988== in use at exit: 52,971,994 bytes in 10,886 blocks
==2137988== total heap usage: 30,553 allocs, 19,667 frees, 91,775,165 bytes allocated
==2137988==
==2137988== LEAK SUMMARY:
==2137988== definitely lost: 0 bytes in 0 blocks
==2137988== indirectly lost: 0 bytes in 0 blocks
==2137988== possibly lost: 0 bytes in 0 blocks
==2137988== still reachable: 52,971,994 bytes in 10,886 blocks
==2137988== of which reachable via heuristic:
==2137988== newarray : 4,264 bytes in 1 blocks
==2137988== suppressed: 0 bytes in 0 blocks
==2137988== Rerun with --leak-check=full to see details of leaked memory
==2137988==
==2137988== For lists of detected and suppressed errors, rerun with: -s
==2137988== ERROR SUMMARY: 19 errors from 2 contexts (suppressed: 0 from 0)
This produced the same results as shown in the attached valgrind log file.
Thanks to Dr.Toby Dylan Hocking for his support on this project. This blog is kindly contributed to R-bloggers.